Welcome to BioResource Index
BioResource Index is an index of commonly used bioinformatics and systems biology databases and software tools. The index covers resources for the analysis of high-throughput genetic, transcriptional, sequence analysis and proteomic profiling. BioResource Index was developed as part of the StemDB database project, funded by the EU FP7 project Eurosystem.
To learn more about BioResource Index and EuroSyStem, click here.
Recent Updates:
There are currently 532 resources detailed on this site, with 709 references and 533 links detailing them.
Our contributors have entered 3 reviews on these resources.
| Name | Description | Type | Platforms | Rating | Last Updated | Links | Detail |
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| GeneProf | GeneProf is a web-based, graphical software suite that allows users to analyse data produced using next-generation sequencing platforms. | Tool : Integrated Analysis : Next-Generation Sequencing : Stem Cell | Web, Download | January 25, 2012 |
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| The MEME Suite | Motif-based sequence analysis tools | Tool : Gene Regulation | Web, Download | December 14, 2011 |
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| Mugen | MUGEN mouse database; animal models of human immunological diseases | Database : Disease | Web | October 19, 2011 |
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| BioProfiling.de | Analytical web portal for high-throughput cell biology | Tool : Gene Regulation | Web | October 19, 2011 |
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| Chipster | Chipster brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH | Tool : Microarray : Expression Analysis : Expression | Java | October 19, 2011 |
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| AS-ALPS | AS-ALPS (Alternative Splicing-induced ALteration of Protein Structure), is aimed at providing useful information to analyze effect of AS on protein interaction and network through alteration of protein structure | Database : Protein Structure : Splicing | Web | October 16, 2011 |
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| MEDIE | MEDIE is an intelligent search engine to retrieve biomedical correlations from MEDLINE, based on indexing by Natural Language Processing and Text Mining technique | Database | Web | October 16, 2011 |
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| EMBRYS | Embryonic Gene Expression Database for Biomedical Research Source | Database : Gene Expression : Expression | Web | October 16, 2011 |
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| Genome Network Platform | Building a human genome network platform- integrating organically global genome information with data from participants in the genome network | Database : Gene Expression : SNP : Genome Annotation : Proteomics | Web | October 16, 2011 |
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| InSilicoDb | "InSilico DB is a complete web-based solution for finding and exporting uniformly processed and curated genomics datasets" | Database : Gene Expression : Microarray : Gene Expression Analysis : Expression | Web | October 7, 2011 |
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| MEME-ChIP | The MEME-ChIP web service is designed to analyze ChIP-seq 'peak regions'--short genomic regions surrounding declared ChIP-seq 'peaks'. | Tool : Next-Generation Sequencing | Web | August 11, 2011 |
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| MATISSE | MATISSE (Module Analysis via Topology of Interactions and Similarity SEts) is a program for detection of functional modules using interaction networks and expression data. | Tool : Gene Expression : Functional Analysis : Gene Expression Analysis : Protein Interaction | Windows, Linux, Java | August 10, 2011 |
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| Stemformatics | a portal to a series of public experiments describing mouse and human stem cells and how they differentiate to become mature cells, tissues and organs. You'll find data from leading stem cell laboratories in a format that is easy to search, easy to visualise and easy to export. Log in to the Workbench to run and save your own analyses. | Database : Gene Expression Analysis : Expression Analysis : Stem Cell | Web | July 6, 2011 |
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| Parkinson DB | Parkinson's disease database | Database : Gene Expression : Disease | Web | June 2, 2011 |
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| MSigDB | Molecular Signatures Database- A collection of gene sets | Database : Integrated Analysis : Gene Expression Analysis : Expression Analysis : Expression | Web, Download | June 2, 2011 |
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| BloodExpress | A database of gene expression in mouse haematopoiesis. | Database : Gene Expression : Stem Cell | Web | June 1, 2011 |
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| ARACNE | ARACNE (Algorithm for the Reconstruction of Accurate Cellular Networks), a novel algorithm, using microarray expression profiles, specifically designed to scale up to the complexity of regulatory networks in mammalian cells | Tool : Network : Systems Biology | Windows, Mac, Linux, Java, Source | June 1, 2011 |
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| Cluster 3.0 | Cluster 3.0 is an enhanced version of Cluster, gene expression clustering software | Tool : Gene Expression : Gene Expression Analysis | Windows, Mac, Linux, UNIX, Source | May 31, 2011 |
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| MoD Tools | MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes | Tool : Gene Regulation | Web | May 31, 2011 |
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| Weeder Web (1.4) | A tool for the discovery of transcription factor binding sites in a set of sequences from co-regulated genes | Tool : Gene Regulation | Web | May 31, 2011 |
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| miRecords | miRecords: an integrated resource for microRNA-target interactions. | Database : RNA | Web | May 31, 2011 |
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| siDRM | siDRM: An online siRNA design tool | Tool : RNA | Web | May 31, 2011 |
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| siRecords | Database of experimentally validated mammalian siRNAs with efficacy ratings | Database : RNA | Web | May 31, 2011 |
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| TargetScan | Search for predicted microRNA targets in mammals | Tool : RNA | Web, Source, Download | May 31, 2011 |
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| TRED | Transcriptional Regulatory Element Database | Database : Gene Regulation | Web | May 31, 2011 |
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| Geneious | Complex data such as entire bacterial genomes or human chromosomes can be stored, visualized and analyzed using a single desktop application that unites pipelines and tools to ensure analyses are easily repeatable. | Chromosomal : Tool : Molecular Biology : Sequence Analysis : Functional Analysis : Next-Generation Sequencing : Sequence : Expression Analysis : Data Analysis : Expression : Multiple Sequence Alignment | Windows, Mac, Linux | May 31, 2011 |
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| GUDMap | The GenitoUrinary Development Molecular Anatomy Project | Gene Expression : Integrated Analysis : Gene Expression Analysis : Image : Expression Analysis : Expression | Web | May 31, 2011 |
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| BioEdit | Biological Sequence Editor | Tool : Sequence Analysis : Sequence | Windows | May 25, 2011 |
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| Eurexpress | Transcriptome-wide acquisition of expression patterns chiefly by means of in situ hybridization (ISH) with non-radioactive probes and will use this data to establish a web-linked, interactive digital transcriptome atlas of embryonic mouse. | Database : Gene Expression : Expression | Web | May 22, 2011 |
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| Human Erythroblast Maturation (HEM) Database | Database of global gene expression analysis of human erythroid progenitors | Database : Expression Analysis : Stem Cell : Expression | Web | May 18, 2011 |
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| GeneXpress | A visualization and analysis tool for gene expression data, integrating clustering, gene annotation, and sequence information. | Tool : Gene Expression Analysis : Expression Analysis | Java | May 17, 2011 |
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| FIRE | A motif discovery and characterization program based on mutual information. | Tool : Sequence Analysis | Web | May 17, 2011 |
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| ChARM | Detection of aneuploidies in array CGH and gene expression microarray data | Chromosomal : Tool : aCGH : Gene Expression Analysis | Download | May 17, 2011 |
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| CellTracer | Cell Tracking software | Tool : Systems Biology | Windows | May 17, 2011 |
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| KEA | Provides users with the ability to link lists of mammalian proteins/genes with the kinases that phosphorylate them. | Tool : Functional Analysis : Systems Biology | Web | May 17, 2011 |
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| Lists2Networks | Integrated analysis of gene/protein lists | Tool : Systems Biology | Web | May 17, 2011 |
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| snavi | Desktop Application for Analysis and Visualization of Large-Scale Cell Signaling Networks | Tool : Systems Biology | Windows, Source | May 17, 2011 |
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| AVIS | AJAX viewer of interactive signaling networks | Tool : Systems Biology | Source | May 17, 2011 |
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| BioModels Database | BioModels Database is a repository of peer-reviewed, published, computational models. | Database : Systems Biology | Web | May 17, 2011 |
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| The Database of Quantitative Cellular Signaling | A repository of models of signaling pathways. | Database : Systems Biology | Web | May 17, 2011 |
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| Jaspar | Database of transcription factor binding profiles | Database : Gene Regulation | Web, Download | May 11, 2011 |
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| Galaxy | Genome Annotation & Analysis System | Database : Genome Annotation | Web | May 2, 2011 |
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| Mayday SeaSight | Next-generation sequencing analysis for the Mayday software suite | Sequence Analysis : Next-Generation Sequencing : Sequence | Java | February 10, 2011 |
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| MIT IGV | The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets | Tool : Genomic Annotation : Next-Generation Sequencing | Java | February 8, 2011 |
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| Savant | Savant: genome browser for high-throughput sequencing data. | Sequence Analysis : Next-Generation Sequencing : Sequence | Web | February 7, 2011 |
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| Modmine | The modENCODE project aims to identify all sequence-based functional elements in the C. elegans and D. melanogaster genomes. modMine is an integrated web resource of data & tools to browse and search modENCODE data. | Database : Gene Expression : Annotation : Sequence Analysis : Functional Analysis : Gene Annotation : Genomic Annotation : Gene Expression Analysis : Next-Generation Sequencing | Web | February 7, 2011 |
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| Ruffus | Ruffus is a lightweight python module to run computational pipelines. | Tool : Workflow | Python | February 7, 2011 |
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| GEDS | Gene Expression Data Simulator | Gene Expression : Gene Expression Analysis | Web | February 7, 2011 |
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| DESeq | DESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression | Tool : Sequence Analysis : Next-Generation Sequencing : Sequence | Windows, Mac, Source | February 7, 2011 |
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| Circos | Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. | Chromosomal : Tool | Perl, Windows, Mac, Linux, UNIX, Source | February 3, 2011 |
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| RACE | Collection of web tools designed to assist with the analysis of DNA microarray data and results. | Tool : Gene Expression : Gene Expression Analysis | Web | February 2, 2011 |
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| MAQ | Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines | Tool : Sequence Analysis : Next-Generation Sequencing : Sequence | Source | January 25, 2011 |
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| Webgestalt | WebGestalt is a "WEB-based GEne SeT AnaLysis Toolkit". It is designed for functional genomic, proteomic and large-scale genetic studies from which large number of gene lists... | Tool : Functional Analysis | Web | January 23, 2011 |
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| Vmatch | A software tool for efficiently solving large scale sequence matching tasks. | Tool : Next-Generation Sequencing | Mac, Linux, UNIX | January 22, 2011 |
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| Bowtie | Bowtie is an ultrafast, memory-efficient short read aligner | Tool : Sequence Analysis : Next-Generation Sequencing : Sequence | Windows, Mac, Linux, Source | January 20, 2011 |
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| caBIG | Integrated informatics portal | Database : Tool : Cancer | Web | January 20, 2011 |
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| BRB-ArrayTools | BRB-ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data | Microarray : Expression Analysis : Expression | Windows | January 20, 2011 |
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| GeneCluster 2.0 | GeneCluster 2.0 expands the data analysis capabilities of GeneCluster 1.0 sample classification tool by adding supervised classification, gene selection and permutation test methods. It includes algorithms for building and testing supervised models using weighted voting (WV) and k-nearest neighbors (KNN) algorithms | Microarray : Expression Analysis : Expression | Windows, Mac, Linux | January 19, 2011 |
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| RMAexpress | RMAExpress is a standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix Genechip® data using the Robust Multichip Average expression summary | Microarray : Data Analysis | Windows, Linux | January 19, 2011 |
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| dChip | Dchip (D-Chip), Analysis and visualization of gene expression and SNP microarrays | Tool : Microarray : SNP : Expression Analysis : Expression | Windows, Mac, Linux, Source | January 19, 2011 |
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| Cyber-t | Cyber-T is a statistics program with a web interface that can be conveniently used on high-dimensional array data for the identification of statistically significant differentially expressed genes | Tool : Gene Expression : Microarray : Gene Expression Analysis | Web | January 19, 2011 |
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| Weka | Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes. | Tool : Expression Analysis | Windows, Mac, Linux, Java, Source | January 19, 2011 |
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| BioWeka | BioWeka is an extension library to the data mining framework Weka for knowledge discovery and data analysis tasks in biology, biochemistry and bioinformatics. | Tool : Gene Expression : Sequence Analysis : Gene Expression Analysis | Java | January 19, 2011 |
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| GenePattern | GenePattern is a powerful genomic analysis platform that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. | Tool : Gene Expression : Functional Analysis : SNP : Gene Expression Analysis : Expression Analysis : Data Analysis | Web, Java, Source | January 19, 2011 |
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| Integrative Genome Viewer | The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets | Tool : Integrated Analysis : Genome : Genome Annotation : Expression : Epigenomics | Windows, Mac, Linux, Java, Source | January 17, 2011 |
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| NextBio | NextBio Basic provides access to a curated, correlated database of public data; integrated literature, clinical trials, and scientific news | Database : Gene Expression : Integrated Analysis : Disease : Proteomics : Epigenomics | Web, Commercial | January 13, 2011 |
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| SCLD | A stem cell lineage database | Database : Stem Cell | Web | January 7, 2011 |
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| NCBI Epigenomics | A public resource for exploring epigenomic data sets | Database : Next-Generation Sequencing : Epigenomics | Web | January 7, 2011 |
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| GEO | Gene Expression Omnibus: a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted | Database : Gene Expression : Microarray | Web | January 7, 2011 |
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| UCSC | The UCSC site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides a portal to the ENCODE project. | Database : Genome Annotation | Web | January 7, 2011 |
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| IKMC | The IKMC database and web portal (www.knockoutmouse.org) serves as the central public web site for IKMC data and facilitates the coordination and prioritization of work within the International Knockout Mouse Consortium | Database : Genetics | Web | January 7, 2011 |
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| GXD | The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse | Database : Gene Expression | Web | January 7, 2011 |
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| Ensembl | The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online | Database : Genome Annotation | Web | January 7, 2011 |
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| miRBase | miRBase is the primary online repository for all microRNA sequences and annotation. | RNA : Sequence | Web | January 7, 2011 |
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| Reactome | Reactome - a curated knowledgebase of biological pathways | Database : Network Analysis : Pathway | Web | January 7, 2011 |
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| BioGRID | BioGRID is an online interaction repository with data compiled through comprehensive curation effort | Database : Interaction | Web | January 7, 2011 |
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| STRING | STRING - Known and Predicted Protein-Protein Interactions | Tool : Protein Interaction | Web | January 7, 2011 |
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| Entrez Gene | Entrez Gene is a searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer | Database : Gene Annotation | Web | January 7, 2011 |
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| Genbank | GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms. | Database : Sequence | Web | January 7, 2011 |
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| ENA | ENA-European Nucleotide Archive provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation | Database : Next-Generation Sequencing : Sequence | Web | January 7, 2011 |
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| SRA | SRA- next-generation sequence archive | Tool : Next-Generation Sequencing : Sequence | Web | January 7, 2011 |
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| DRA | DDBJ Sequence Read Archive (DRA) is an archive database for output data generated by next-generation sequencing machines including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD® System, and others. | Database : Next-Generation Sequencing : Sequence | Web | January 7, 2011 |
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| NSDC | Under the International Nucleotide Sequence Database Collaboration globally comprehensive public domain nucleotide sequence is captured, preserved and presented. | Next-Generation Sequencing : Sequence | Web | January 7, 2011 |
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| MACS | Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer | Tool : Next-Generation Sequencing | Python | January 7, 2011 |
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| ENCODEdb | This portal provides users a single, unified point-of-access to data generated by the ENCODE Consortium, regardless of which public database the primary data is housed in | Database | Web | January 6, 2011 |
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| Epigraph | EpiGRAPH is a software for genome and epigenome analysis | Tool : Sequence Analysis : Next-Generation Sequencing | Web | January 6, 2011 |
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| GENIO/logo | RNA/DNA & Amino Acid Sequence Logos | Tool : RNA : Protein Sequence : Sequence | Web | December 22, 2010 |
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| pLogo | Protein Sequence Logos using Relative Entropy | Tool : Protein Sequence : Sequence | Web, Source | December 22, 2010 |
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| WebLogo | A web-based application for the generation of sequence logos | Tool : Sequence | Web, Source | December 22, 2010 |
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| SeqLogo | seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo | Tool : Sequence | Windows, Mac, Source | December 22, 2010 |
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| SeeGraph | SeeGraph is a package for the interactive visualization and analysis of graphs | Tool | Windows, Linux | December 22, 2010 |
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| Trans-Proteomic Pipeline | The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics | Tool : Proteomics : Data Analysis | Windows, Mac, Linux, Source | December 21, 2010 |
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| Bioinformatics Resource Manager | Bioinformatics Resource Manager automates multidisciplinary data mining processes used for high-throughput molecular profiling. | Tool : Integrated Analysis : Expression Analysis | Java | December 20, 2010 |
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| Ontological Discovery Environment | The Ontological Discovery Environment allows users to integrate phenotype centered gene sets across species, tissue and experimental platform | Database : Tool : Microarray : Integrated Analysis : Gene Expression Analysis : Data Analysis | Web | December 20, 2010 |
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| SBEAMS | Systems Biology Experiment Analysis Management System (SBEAMS), enables MIAME-compliant storage, management, analysis, and integration of high-throughput genomic expression dat | Database : Gene Expression : Microarray : Proteomics : Expression | Web, Source | December 20, 2010 |
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| BLASTO | BLAST on Orthologous groups (BLASTO), a modified BLAST tool for searching orthologous group data | Tool : Sequence Analysis : Sequence | Web | December 20, 2010 |
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| edgeR | edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. | Tool : Sequence Analysis : Next-Generation Sequencing | Windows, Mac, Linux, Source, Download | December 16, 2010 |
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| iScMiD | Integrated Stem Cell Molecular Interaction Database (iScMiD) | Database : Stem Cell | Web, Download | December 14, 2010 |
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| STITCH | STITCH is a resource to explore known and predicted interactions of chemicals and proteins | Proteins : Protein Interaction | Web | December 14, 2010 |
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| CellProfiler | CellProfiler is designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically | Tool : Image : Image Analysis | Windows, Mac, Linux, Source | November 25, 2010 |
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| Cell Profiler Analyst | CellProfiler Analyst is free open-source software for exploring and analyzing large, high-dimensional image-derived data | Image : Image Analysis | Windows, Mac, Linux, Source | November 25, 2010 |
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| Embryonic stem cells database (ESCDb) | Gathers chromatin immunoprecipitation on chip and sequencing data together with perturbation experiments conducted on both human and mouse (ESC) and embryonic carcinoma cells (EC) | Database : Stem Cell | Web | November 25, 2010 |
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| The KTH-Package | A collection of tools to make microarray analysis easier | Tool : Gene Expression : Microarray : Gene Expression Analysis | Windows, Mac | October 25, 2010 |
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| GATE | Grid Analysis of Time Series Data | Tool : Gene Expression : Microarray : Gene Expression Analysis : Stem Cell | Windows, Mac, Linux, Java | October 25, 2010 |
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| CARMAWeb | A comprehensive R- and Bioconductor-based web service for microarray data analysis | Tool : Gene Expression : Microarray : Functional Analysis : Gene Expression Analysis : Data Analysis | Web | October 25, 2010 |
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| The Ellington Lab Aptamer Database | Aptamers are DNA or RNA molecules select that have been identified by their ability to bind other molecules | Database : RNA : Sequence | Web | October 19, 2010 |
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| SKY/M-FISH and CGH Database | A database for sharing and comparing molecular cytogenetics data | Database : Chromosomal : Cancer | Web | October 19, 2010 |
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| Telomerase Database | A web-based database to study the function, structure and evolution of telomerase ribonuclearprotein | Database : Genomic Annotation : Protein Structure | Web | October 19, 2010 |
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| R-GSEA | Gene set enrichment analysis with R. | Tool : Functional Analysis | Source, Download | October 19, 2010 |
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| GSEA | Gene Set Enrichment Analysis- | Tool : Functional Analysis : Expression Analysis | Java, Source | October 19, 2010 |
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| ProSplicer | Alternative splicing database produced from variant protein and gene expression patterns | Database : Splicing | Web | October 19, 2010 |
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| Home Page | Human Transcriptome Database for Alternative Splicing | Database : Splicing | Web | October 19, 2010 |
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| ASSP | Alternative Splice Site Prediction | Tool : Sequence Analysis : Splicing | Web | October 19, 2010 |
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| ASTD | Alternative Splicing and Transcipt Diversity database | Database : Sequence : Splicing | Web, Download | October 19, 2010 |
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| ScanPS Web Server | SCANPS performs iterative profile searching similar to PSI-BLAST but with full dynamic programing on each cycle and on-the-fly estimation of significance | Tool : Sequence Analysis : Protein Sequence | Web | October 15, 2010 |
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| PASS2 | PASS2 contains alignments of protein structures at the superfamily level | Database : Proteins : Protein Sequence : Protein Structure : Sequence | Web | October 15, 2010 |
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| UniVec | A database of cloning vector nucleic acid sequences that can be used to identify segments of sequence that of vector origin | Tool : Sequence Analysis | Web | October 15, 2010 |
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| AceDB | AceDB is a flexible database designed to store genomic data | Database : Genome : Genomic Annotation | Windows, Mac, Linux, UNIX, Source, Download | October 15, 2010 |
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| Stem Cell Mesa | Stem Cell Microarray Data Server | Database : Gene Expression : Stem Cell : Expression | Web | September 16, 2010 |
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| Tablet | Tablet?next generation sequence assembly visualization | Tool : Sequence Analysis : Next-Generation Sequencing : Sequence : Genome Assembly | Windows, Mac, Linux, Java, UNIX | August 17, 2010 |
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| WWW Signal Scan | Web version of SignalScan, a computer program that scans DNA sequences for eukaryotic transcriptional elements | Tool : Gene Regulation : Sequence Analysis : Sequence | Web | August 6, 2010 |
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| ConSequenceS | This is a method for searching and aligning databases of consensus sequences | Tool : Sequence Analysis : Sequence | Web | August 6, 2010 |
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| Exalign | Exalign is a tool that performs alignments of gene exonic structures. | Tool : Sequence Analysis : Gene Annotation : Gene Prediction : Sequence | Web | August 6, 2010 |
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| SECISaln | SECISaln will predict a eukaryotic [selenocysteine] SECIS element in a nucleotide sequence | Tool : Protein Annotation : Proteins : Protein Signatures | Web | August 6, 2010 |
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| FSA | Fast statistical alignment of biological sequences | Tool : Sequence Analysis : Sequence | Web | August 6, 2010 |
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| PubMed | PubMed comprises approximately 20 million citations for biomedical literature from MEDLINE, life science journals, and online books. PubMed citations and abstracts include the fields of medicine, nursing, dentistry, veterinary medicine, the health care system, and preclinical sciences. PubMed also provides access to additional relevant Web sites and links to the other NCBI molecular biology resources. PubMed is a free resource that is developed and maintained by the National Center for Biotechnology Information (NCBI), at the U.S. National Library of Medicine (NLM), located at the National Institutes of Health (NIH). | Database : Literature Mining | Web | August 6, 2010 |
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| Venny | Venny is a simple web-based tool for creating Venn diagrams of up to four different lists. Venny automatically calculates the overlaps for all possible permutations of the given datasets (say, lists of gene symbols or probe ID's). | Tool | Web | August 6, 2010 |
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| SWISS-MODEL Repository | The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL. | Database | Web | August 6, 2010 |
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| CrossChip | A microarray analysis often involves comparing data across different platforms. Unfortunately, significant differences exist among these platforms and data cannot be combined directly | Integrated Analysis | Java | August 6, 2010 |
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| iHOP | Information Hyperlinked over Proteins. A gene network for navigating the literature | Database : Protein Annotation : Literature Mining | Web | August 6, 2010 |
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| WebGestalt | WebGestalt is a "WEB-based GEne SeT AnaLysis Toolkit". WebGestalt incorporates information from different public resources and provides an easy way for biologists to make sense out of large sets of genes | Chromosomal : Tool : Gene Expression | Web | August 6, 2010 |
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| CisGenome | An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis. | Tool : Next-Generation Sequencing | Windows, Mac, Linux, Source |
(1 review) |
June 24, 2010 |
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| R | Software enviroment for statistical calculations and graphics | Tool | Windows, Mac, UNIX |
(1 review) |
January 7, 2011 |
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| Bioconductor | Central bioinformatics project that runs within R | Tool : Data Analysis | Windows, Mac, Linux, Source |
(1 review) |
June 24, 2010 |
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| Praline | PRALINE is a multiple sequence alignment program with many options to optimise the information for each of the input sequences; e.g. homology-extended alignment, predicted secondary structure and/or transmembrane structure information. | Database : Tool : Sequence Analysis | Web | August 6, 2010 |
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| PlasMapper | The PlasMapper server automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input. | Tool : Molecular Biology : Sequence Analysis | Web, Source, Download | August 6, 2010 |
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| WebCutter 2.0 | Restriction map prediction software | Tool : Molecular Biology : Sequence Analysis | Web | August 6, 2010 |
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| PROMALS3D | PROMALS3D constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints | Database : Proteins : Sequence Analysis : Functional Analysis : Gene Annotation : Protein Sequence | Web | August 6, 2010 |
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| PairsDB | PairsDB is a collection of protein sequences and the BLAST and PSI-BLAST alignments between them | Database : Sequence Analysis | Web | August 6, 2010 |
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| Rankprop | A web server for protein remote homology detection | Proteins : Sequence Analysis : Data Format | Web, Source | August 6, 2010 |
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| PDBSum | PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB). | Database : Proteins : Protein Structure | Web | August 6, 2010 |
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| Annotation-Modules | A tool for finding significant combinations of multisource annotations in gene lists | Annotation | Web | August 6, 2010 |
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| AutoSOME | AutoSOME is a new unsupervised multidimensional clustering method for identifying clusters of diverse shapes and sizes from large numerical datasets | Gene Expression Analysis : Expression Analysis : Data Analysis | Java, Download | August 6, 2010 |
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| GENtle | GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more | Molecular Biology | Windows, Mac, Linux, Source | August 5, 2010 |
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| DAVID | Annotation, visualisation and functional enrichment and functional discovery in sets of genes | Tool : Functional Analysis | Web | August 3, 2010 |
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| Pfam | The Pfam protein families database. | Database : Protein Annotation : Protein Signatures | Web | July 28, 2010 |
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| Mayday | Mayday is a workbench for visualization, analysis and storage of microarray data | Gene Expression : Microarray : Integrated Analysis : Gene Expression Analysis : Expression Analysis | Java | July 27, 2010 |
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| ProfCom | ProfCom automatically generates statistically valid hypotheses / biological models from gene or protein lists supplied by the user. This knowledge can help to improve your understanding of genetic mechanisms involved in biological phenomena under study. | Tool : Modelling | Web | June 29, 2010 |
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| GeneCards | GeneCards is a searchable, integrated, database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes | Database : Gene Annotation | Web | June 25, 2010 |
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| caGEDA | A web application for the integrated analysis of global gene expression patterns in cancer | Tool : Integrated Analysis : Disease : Cancer | Web | June 25, 2010 |
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| Cellminer | CellMiner? is a web application that facilitates systems biology through the retreival and integration of the various molecular data sets | Integrated Analysis | Web | June 25, 2010 |
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| LefMiner | LeFEMiner determines which sets of functionally related genes (ie. gene categories or ensembles) are most biologically related to the observed biology or state of the samples | Tool : Functional Analysis | Windows, Mac, Linux, Source | June 24, 2010 |
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| GlobalTest | Testing groups of covariates/features for association with a response variable with application to gene set testing | Tool : Functional Analysis | Windows, Mac, Linux, Source | June 24, 2010 |
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| Apex Proteomics | The APEX Quantitative Proteomics Tool, is a free and open source Java implementation of the APEX technique for the quantitation of proteins based on standard LC- MS/MS proteomics data (Lu et al., Nature Biotech., 25(1):117-124, 2007). | Tool : Proteomics | Windows, Mac, Linux, Source | June 24, 2010 |
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| Genesis | A platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments. | Tool : Gene Expression : Microarray : Integrated Analysis | Windows, Linux, Java | June 24, 2010 |
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| Magnolia | Magnolia provides PFGRC array users with a series of intelligent entry form to collect the information or parameters of experiment, bio-source, sample, probe, slide, scan, expression, and normalization, which isMIAME compliant | Tool : Microarray : Expression | Windows | June 24, 2010 |
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| Katsura | The Katsura tool is a free open source Java application designed to overlay gene expression data, comparative genomics data, or quantitative shotgun proteomics data onto metabolic pathway | Chromosomal : Tool : aCGH : Gene Expression : Microarray : Network Analysis : Pathway | Windows, Mac, Linux, Source | June 24, 2010 |
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| GeneTrack | GeneTrack is a bioinformatics software package for storing, querying and visualizing interval oriented data | Chromosomal : Tool | Python | June 24, 2010 |
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| AMOS | Manipulation of input and output files related to whole-genome shotgun assembly. | Tool : Genome Assembly | UNIX | June 24, 2010 |
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| Celera Assembler | Celera Assembler can reconstruct long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing | Tool : Genome Assembly | UNIX | June 24, 2010 |
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| Elvira | High throughput assembly of amplicon reads for virus-sized genomes | Tool : Genome Assembly | June 24, 2010 |
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| Flexarray | FlexArray is a Microsoft Windows software package for statistical analysis of microarray expression data | Tool : Gene Expression : Microarray | Windows | June 24, 2010 |
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| Ginkgo | Ginkgo is a spotted microarray data pre-processing platform featuring analysis functionalities for CGH and expression data. | Chromosomal : Tool : aCGH : Gene Expression : Microarray | Windows, Linux, Source | June 24, 2010 |
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| RMA Express | RMAExpress is a standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix Genechip® data using the Robust Multichip Average expression summary and to carry out quality assessment using probe-level met | Tool : Gene Expression : Microarray | Windows, Linux | June 24, 2010 |
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| SiSA | SISA allows you to do statistical analysis directly on the Interne | Tool : Data Analysis | Web | June 24, 2010 |
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| TRANSFAC | BLK TRANSFAC is an internationally unique knowledgebase containing data on transcription factors, their experimentally-proven binding sites, and regulated genes | Tool : Gene Regulation | Web, Commercial, Download | June 24, 2010 |
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| Limma | Linear models for gene expression. Microarray differential gene indentification package | Tool : Gene Expression : Microarray | Windows, Mac, UNIX | June 24, 2010 |
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| MeV | Multiexperiment Viewer Analysis visualisation and mining of genomic data | Tool : Gene Expression : Microarray | Windows, Mac, Linux | June 24, 2010 |
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| GeneNetwork | GeneNetwork consists of linked resources and analysis tools for systems genetics | Tool : Systems Biology : Genetics | Web | June 24, 2010 |
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| Gillespie Simulator | A graphical user interface for simulations of stochastic network models and statistical analysis on the results. | Tool : Modelling | Windows, Mac, Linux | June 24, 2010 |
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| ENFIN | A Joint Research Program covering the fields of Discrete Function Prediction, Network Reconstruction, Systems-Level Modeling | Tool : Modelling : Network | Web | June 24, 2010 |
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| XPPAUT | Provides numerical solvers and analysis tools for models described by discrete and continuous equations. | Tool : Modelling | Windows, Mac, Linux, Source | June 24, 2010 |
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| Beta Cell Biology Consortium | Beta Cell Genomics: The genomics section contains detailed information about genes, mRNA expression studies, and ChIP studies. | Database : Stem Cell | Web | June 24, 2010 |
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| SCDb | SCDB- the stem cell database | Database : Stem Cell | Web | June 24, 2010 |
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| ASTD | Alternative Splicing and Transcript Diversity database | Tool : Sequence Analysis | Web | June 24, 2010 |
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| AltAnalyze | AltAnalyze works with conventional microarrays (3' arrays) but also includes specialized functions for exon (Affymetrix Exon 1.0 and Gene 1.0) and junction arrays to identify predicted alternative splicing or alternative promoter change | Tool : Expression Analysis | Windows, Mac, Linux, Source | June 24, 2010 |
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| ASPIC | ASPic (Alternative Splicing Prediction) is a web-based tool to detect the exon-intron structure of a gene by comparing its genomic sequence to the related cluster of EST | Tool : Sequence Analysis | Web | June 24, 2010 |
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| Systems Biology Workbench | SBW is a framework including different software packages for network modelling, analysis, visualization and data manipulation. | Tool : Modelling : Network Analysis | Windows, Mac, Linux | June 24, 2010 |
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| CASCAD | CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences. | Tool : SNP | Web | June 24, 2010 |
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| SNPselector | SNPselector: a web tool for selecting SNPs for genetic association studies | Tool : SNP | Web | June 24, 2010 |
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| SNPeffect | Molecular phenotyping of human SNPs and disease mutations | Tool : SNP | Web | June 24, 2010 |
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| SNPmasker | SNPmasker 1.0 is a program to mask all SNPs in given sequence using information of dbSNP. | Tool : SNP | Web | June 24, 2010 |
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| FeatureScam | Searching for sequence similarity by comparing physico-chemical properties of DNA | Database : Sequence | Web | June 24, 2010 |
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| TraceTuner | Tool : Molecular Biology | June 24, 2010 |
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| Sky, M-FISH and aCGH database | aCGH and Sky and m-fish database | Database : Genomic Aberration : Chromosomal : Disease : Cancer | Web | June 24, 2010 |
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| ACUTS | ACUTS: compilation of Ancient Conserved UnTranslated Sequences | Database : Sequence | Web | June 24, 2010 |
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| dbSTS | dbSTS is an NCBI resource that contains sequence data for short genomic landmark sequences or Sequence Tagged Sites (sequences unique in the genome) | Database : Sequence | Web | June 24, 2010 |
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| dbEST | dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms | Database : Sequence | Web | June 24, 2010 |
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| DDBJ | DNA Databank of Japan | Database : Sequence | Web | June 24, 2010 |
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| EMBL | The EMBL Nucleotide Sequence Database (also known as EMBL-Bank) constitutes Europe's primary nucleotide sequence resource | Database : Sequence | Web | June 24, 2010 |
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| Lucy2 | A graphical tool for cleaning data produced by automated Sanger DNA sequencers prior to sequence assembly and other downstream uses. | Tool : Sequence Analysis | Windows, Mac, Linux | June 24, 2010 |
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| Lucy | A tool for cleaning data produced by automated Sanger DNA sequencers prior to sequence assembly and other downstream uses. | Tool : Sequence Analysis | UNIX | June 24, 2010 |
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| TIGR Assembler | Enabled the first published whole-genome assembly of a free-living organism in 1995. Last revised in 2003. | Tool : Sequence Analysis | June 24, 2010 |
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| GenScan (MIT) | Identification of complete gene structures in genomic DNA | Tool : Sequence Analysis | Web, Download | June 24, 2010 |
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| NCBI Genome Workbench | NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data | Tool : Sequence Analysis | Windows, Mac, Linux | June 24, 2010 |
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| Lasergene | Lasergene is a comprehensive DNA and protein sequence analysis software suite comprised of seven applications which include functions ranging from sequence assembly and SNP detection, to automated virtual cloning and primer design. | Tool : Sequence Analysis | Windows, Mac, Commercial | June 24, 2010 |
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| W2H | W2H is a free WWW interface to sequence analysis software tools like the GCG-Package (Genetic Computer Group), EMBOSS (European Molecular Biology Open Software Suite) or to derived services (such as HUSAR, Heidelberg Unix Sequence Analysis Resources). | Tool : Sequence Analysis | Web | June 24, 2010 |
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| Repeat Masker | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences | Tool : Sequence Analysis | Web, Download | June 24, 2010 |
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| Emboss Explorer | EMBOSS explorer is a web-based graphical user interface to the EMBOSS suite of bioinformatics tools. It is exceedingly simple to install, configure, maintain and use | Tool : Sequence Analysis | Web, Download | June 24, 2010 |
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| SRS@EBI | Sequence Integration and Analysis Service @EBI | Tool : Sequence Analysis | Web | June 24, 2010 |
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| Blat | BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments | Tool : Sequence Analysis | Windows, Mac, Linux, Source | June 24, 2010 |
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| EMBOSS | Sequence analysis suite | Tool : Sequence Analysis | Windows, Mac, Linux, Source | June 24, 2010 |
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| Jemboss | A graphical viewer for EMBOSS | Tool : Sequence Analysis | Java | June 24, 2010 |
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| Blast | Sequence searching and alignment tool | Tool : Sequence Analysis | Web, Windows, Mac, Linux | June 24, 2010 |
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| RNAmod db | A comprehensive listing of post-transcriptionally modified nucleosides from RNA | Database : RNA | Web | June 24, 2010 |
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| Jarnac | Jarnac is a language for modelling and manipulating network models. | Tool : Modelling | Windows, Mac, Linux | June 24, 2010 |
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| tRNAdb | tRNAdb 2009 is the new version of "Compilation of tRNA sequences and tRNA genes". | Database : RNA | Web | June 24, 2010 |
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| Biocatalogue | The BioCatalogue: providing a curated catalogue of Life Science Web Services | Database : Tool : Integrated Analysis | Web | June 24, 2010 |
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| CellDesigner | CellDesignerTM: A modeling tool of biochemical networks | Tool : Network Analysis : Gene Regulation | Java | June 24, 2010 |
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| Re1db | The RE1db project has sought to use bioinformatic techniques to help predict genes that are regulated by the repressor element 1(RE1)/RE1 silencing transcription factor (REST) system | Tool : Gene Regulation | Web | June 24, 2010 |
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| Carrie | CARRIE takes two condition microarray data and applies promoter analysis to infer the stimulated/repressed transcriptional regulatory network. | Tool : Network Analysis : Gene Regulation : Sequence Analysis | Web | June 24, 2010 |
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| CompareProspector | CompareProspector conserved regulatory motif discovery package | Tool : Gene Regulation : Sequence Analysis | Web | June 24, 2010 |
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| CMA | Composite Module Analyst: Defining promoter models based on the composition of transcription factor binding sites and their pairs. | Tool : Gene Regulation : Sequence Analysis | Web | June 24, 2010 |
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| Bioprospector | Discover conserved motifs in upstream regulatory regions of co-expressed genes | Tool : Gene Regulation : Sequence Analysis | Web | June 24, 2010 |
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| AffyProbeMiner | Generate a collection of complete coding sequences and rtegroup Affymetrix probes | Database : Microarray : Annotation | Web | June 24, 2010 |
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| GlycoSuiteDB | Glycoproteomics made easier | Database : Proteomics | Web | June 24, 2010 |
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| MPDB | Membrane Protein Databank | Database : Proteomics | Web | June 24, 2010 |
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| WORLD-2DPAGE Repository | A public repository, standards compliant, for proteomics image data published in the literature | Database : Proteomics | Web | June 24, 2010 |
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| MIAPEGelDB | MIAPEGelDB is intended to help end-users to write such MIAPE documents, through a self-documenting web interface The MIAPE documents specifies the minimum information to report when describing or publishing a proteomics experiment. | Database : Proteomics | Web | June 24, 2010 |
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| CROPPER | A Fully Automated Software for the Confident Identification of Human Peptides from Tandem Mass Spectra | Database : Proteomics | Web | June 24, 2010 |
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| VisANT | VisANT: an online visualization and analysis tool for biological interaction data. | Database : Interaction | Java | June 24, 2010 |
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| MAPU 2.0 | MAPU 2.0: high-accuracy proteomes mapped to genomes | Database : Proteomics | Web | June 24, 2010 |
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| MDscan | A Fast and Accurate Motif Finding Algorithm With Applications To Chromatin Immunoprecipitation Microarray Experiments | Tool : Gene Regulation : Sequence Analysis | Web | June 24, 2010 |
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| ModBase | MODBASE is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. | Database : Protein Structure | Web | June 24, 2010 |
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| SCOP | The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. | Database : Protein Structure | Web | June 24, 2010 |
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| PDBTM | Transmembrane protein selection of the Protein Data Bank (PDB) | Database : Protein Structure | Web | June 24, 2010 |
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| ProSas | The ProSAS (Protein Structure and Alternative Splicing) database provides a unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms | Database : Protein Structure | Web | June 24, 2010 |
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| wwPDB | The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. | Database : Protein Structure | Web | June 24, 2010 |
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| DisProt | DisProt: the Database of Disordered Proteins | Database : Protein Structure | Web | June 24, 2010 |
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| MutaProt | Comparison of PDB files which differ by point mutations | Database : Protein Structure | Web | June 24, 2010 |
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| HSSP | The HSSP database is a database of homology-derived secondary structure of proteins | Database : Protein Structure | Web | June 24, 2010 |
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| CSD | The world repository of small molecule crystal structures | Database : Protein Structure | Web | June 24, 2010 |
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| CN3D | Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service | Database : Protein Structure | Windows, Mac, UNIX | June 24, 2010 |
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| Molecules to Go | NCBI search tool | Database : Protein Structure | Web | June 24, 2010 |
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| SBASE | SBASE is a collection of protein domain sequences collected from the literature, from protein sequence databases and from genomic databases | Database : Protein Signatures | Web | June 24, 2010 |
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| Swiss-Pdb Viewer | Load and displaymolecular structures | Database : Protein Structure | Windows, Mac | June 24, 2010 |
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| ProDom | ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Data | Database : Protein Signatures | Web | June 24, 2010 |
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| PRINTS | PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite | Database : Protein Signatures | Web | June 24, 2010 |
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| Panther | The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions | Database : Protein Signatures | Web | June 24, 2010 |
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| Gene3d | Gene3D: modelling protein structure, function and evolution. | Database : Protein Signatures | June 24, 2010 |
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| cath | CATH is a manually curated classification of protein domain structures | Database : Protein Signatures | Web | June 24, 2010 |
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| BLOCKS | Blocks are ungapped multiple alignments of segments of related protein sequences that correspond to the most conserved regions of proteins. | Database : Protein Signatures | Web | June 24, 2010 |
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| PROSITE | PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them | Database : Protein Signatures | Web | June 24, 2010 |
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| Interpro | InterPro is an integrated database of predictive protein "signatures" used for the classification and automatic annotation of proteins and genomes | Database : Protein Signatures | Web | June 24, 2010 |
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| Uniprot | comprehensive, high-quality and freely accessible resource of protein sequence and functional information | Database : Protein Annotation | Web | June 24, 2010 |
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| HPRD | The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome | Tool : Protein Interaction | Web | June 24, 2010 |
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| MINT | Welcome to MINT, the Molecular INTeraction database. MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators | Tool : Protein Interaction | Web | June 24, 2010 |
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| DIP | The DIPTM database catalogs experimentally determined interactions between protein | Tool : Protein Interaction | Web | June 24, 2010 |
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| Relibase | Easy searching of protein-ligand complexes | Tool : Sequence Analysis | Web | June 24, 2010 |
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| MIPS PPI | The MIPS Mammalian Protein-Protein Interaction Database is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators | Database : Interaction | Web | June 24, 2010 |
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| IntAct | IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available. | Database : Interaction | Web | June 24, 2010 |
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| BMM Domain Fishing | This server looks for recognizable protein domains in your amino acid sequence. | Tool : Sequence Analysis | Web | June 24, 2010 |
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| Human Protein Atlas | The human protein atlas shows expression and localization of proteins in a large variety of normal human tissues, cancer cells and cell lines with the aid of immunohistochemistry (IHC) images and immunofluorescence (IF) confocal microscopy images. | Database : Protein Annotation | Web | June 24, 2010 |
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| WormPep | Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project. | Database : Protein Annotation | Web | June 24, 2010 |
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| HUGE | A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project | Database : Protein Annotation | Web | June 24, 2010 |
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| PMD | The Protein Mutant Database (PMD) that we are constructing covers natural as well as artificial mutants, including random and site-directed ones, for all proteins except members of the globin and immunoglobulin f | Database : Protein Annotation | Web | June 24, 2010 |
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| Smart | SMART (Simple Modular Architecture Research Tool) is a web tool for the identification and annotation of protein domains | Database : Protein Annotation | Web | June 24, 2010 |
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| ProtoNet | ProtoNet: Automatic hierarchical classifications of proteins | Database : Protein Annotation | Web | June 24, 2010 |
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| PIRSF | The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships | Database : Protein Annotation | Web | June 24, 2010 |
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| SUPERFAMILY | SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes. | Database : Protein Annotation | Web | June 24, 2010 |
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| Uniprot | The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. | Database : Protein Annotation | Web | June 24, 2010 |
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| EPD | The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters | Database : Gene Regulation | Web | June 24, 2010 |
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| CODHOP | PCR primers designed from protein multiple sequence alignments | Tool : Molecular Biology | Web | June 24, 2010 |
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| Primer3 | Pick primers from a DNA sequence | Tool : Molecular Biology | Web, Download | June 24, 2010 |
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| AmplifX | The main purpose of AmplifX is to search through a collection of primers | Tool : Molecular Biology | Windows, Mac | June 24, 2010 |
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| PrimerZ | PrimerZ: streamlined primer design for promoters, exons and human SNPs | Tool : Molecular Biology | Web | June 24, 2010 |
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| SNPBox | SNPbox is a modular software package that automates the design of PCR primers for large-scale amplification and sequencing projects | Tool : Molecular Biology | Web | June 24, 2010 |
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| PerlPrimer | PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. | Tool : Molecular Biology | Web | June 24, 2010 |
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| PASSML | A computer program called PASSML ('Phylogeny and Secondary Structure using Maximum Likelihood') has been developed to implement an evolutionary model that combines protein secondary structure and amino acid replacement | Tool : Sequence Analysis : Phylogeny | Source | June 24, 2010 |
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| PHYLIP | PHYLIP is a free package of programs for inferring phylogenies | Tool : Sequence Analysis : Phylogeny | Windows, Mac, Linux, Source | June 24, 2010 |
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| MOLPHY | MOLPHY: A Computer Program Package for Molecular Phylogenetics | Tool : Sequence Analysis : Phylogeny | UNIX, Source | June 24, 2010 |
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| PAML 4 | PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. | Tool : Sequence Analysis : Phylogeny | Windows, Mac, Linux | June 24, 2010 |
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| PAUP *4.0 | Software package for inference of evolutionary trees | Tool : Sequence Analysis : Phylogeny | Windows, Mac, UNIX, VMS | June 24, 2010 |
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| Phase | PHASE is a package that performs molecular phylogenetic inference. The software seeks to accurately compare molecular sequences to determine the likely evolutionary relationships between a group of species | Tool : Sequence Analysis : Phylogeny | Windows, Linux, Source | June 24, 2010 |
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| Beast | BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree | Tool : Sequence Analysis : Phylogeny | Windows, Mac, UNIX, Source | June 24, 2010 |
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| Mac5 | MAC5 implements MCMC sampling of the posterior distribution of tree topologies from DNA sequences containing gaps by using a five state model of evolution (the four nucleotides and the gap character) | Tool : Sequence Analysis : Phylogeny | Windows, Mac, UNIX, Source | June 24, 2010 |
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| PhyloPat | Phylogenetic patterns show the presence or absence of certain genes or proteins in a set of sp | Tool : Sequence Analysis : Phylogeny | Web | June 24, 2010 |
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| MrBayes | MrBayes is a program for the Bayesian estimation of phylogeny | Tool : Sequence Analysis : Phylogeny | Web | June 24, 2010 |
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| FigTree | FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures | Tool : Sequence Analysis : Phylogeny | Java | June 24, 2010 |
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| TreeBase | TreeBASE is a relational database of phylogenetic information | Tool : Sequence Analysis : Phylogeny | Web | June 24, 2010 |
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| BAMBE | Bayesian Analysis in Molecular Biology and Evolution (BAMBE) is a free software package for the Bayesian analysis of phylogenies | Tool : Sequence Analysis : Phylogeny | Windows, UNIX | June 24, 2010 |
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| JCVI Primer Designer | High throughput PCR primer design software. | Tool : Molecular Biology | June 24, 2010 |
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| KEGG | KEGG: Kyoto Encyclopedia of Genes and Genomes | Database : Network Analysis : Pathway | Web | June 24, 2010 |
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| Genstruct | Genstruct: automating and optimizing the pharmaceutical drug development process. | Tool : Network Analysis : Pathway | Web, Commercial | June 24, 2010 |
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| Ingenuity | Technologies that help life science researchers more effectively search, explore, visualize, and analyze biological and chemical findings related to genes, proteins, and small molecules (e.g. drugs) | Database : Tool : Network Analysis : Pathway | Web, Commercial | June 24, 2010 |
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| KEGG | Pathway maps | Database : Network Analysis : Pathway | Web | June 24, 2010 |
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| Exonerate | Exonerate is a generic tool for pairwise sequence comparison | Tool : Sequence Analysis | Web | June 24, 2010 |
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| HCOP | HGNC Comparison of Orthology Predictions | Tool : Sequence Analysis | Web | June 24, 2010 |
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| MitoDat | MitoDat - Mendelian Inheritance and the Mitochondrion | Database : Organelle | Web | June 24, 2010 |
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| GOBASE | GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts | Database : Organelle | Web | June 24, 2010 |
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| CTD | The Comparative Toxicogenomics Database (CTD) elucidates molecular mechanisms by which environmental chemicals affect human disease | Database : Ontology | Web | June 24, 2010 |
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| PeroxisomeDB | PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome | Database : Organelle | Web | June 24, 2010 |
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| Ontology Evolution Explorer (OnEX) | The Ontology Evolution Explorer (OnEX) is a web-based system for exploring ontology changes. | Tool : Ontology | Web | June 24, 2010 |
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| COBrA | Browse and search and edit GO and OBO formatted ontology information | Tool : Ontology | Java | June 24, 2010 |
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| BioMagResBank | A repository for Data from NMR Spectroscopy on Proteins, Peptides and Nucleic Acids | Database : Proteomics | Web | June 24, 2010 |
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| LNA tools | LNA (Locked Nucleic Acid) melting temperature prediction tool | Tool : Molecular Biology | Web | June 24, 2010 |
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| Expression Profiler | Expression Profiler: An open extensible web-based collaborative platform for microarray gene expression, protein protein interaction and next gen sequence | Tool : Gene Expression : Microarray : Next-Generation Sequencing | Web | June 24, 2010 |
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| CLC Workbench | CLC Genomics Workbench, for analyzing and visualizing Next Generation Sequencing data, incorporates cutting-edge technology and algorithms | Tool : Next-Generation Sequencing | Web, Commercial | June 24, 2010 |
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| ERANGE | ERANGE is a Python package for doing RNA-seq and ChIP-seq | Tool : Next-Generation Sequencing | Mac, Linux, Python | June 24, 2010 |
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| SISSRS | SISSRs (Site Identification from Short Sequence Reads), a novel algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments | Tool : Next-Generation Sequencing | Perl | June 24, 2010 |
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| Wold Lab Software Suite | The Wold Bioinformatics Lab Software Suite | Tool : Next-Generation Sequencing | Python | June 24, 2010 |
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| QuEST | QuEST is a Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitations (ChIP-Seq or ChIPseq). | Tool : Next-Generation Sequencing | Source | June 24, 2010 |
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| ChIPDiff | Genome-wide Identification of Differential Histone Modification Sites from ChIP-Seq Data". Bioinformatics, 24:2344-2349 | Tool : Next-Generation Sequencing | Source | June 24, 2010 |
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| FindPeaks | FindPeaks: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology | Tool : Next-Generation Sequencing | Java | June 24, 2010 |
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| Biolayout Express | BioLayout Express3D is a tool for the visualization and analysis of networks derived from biological systems | Tool : Network Analysis | Windows, Mac, Linux, Source | June 24, 2010 |
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| PBMice | PBmice provides integrated information of PiggyBac insertional mutations and their characterizations in mice | Database : Gene Mutant | Web | June 24, 2010 |
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| chipSeq Peak Finder | The ChIP-Seq peak finder version 2.0 and higher is actually now part of the ERANGE package | Tool : Next-Generation Sequencing | Mac, Linux, Python | June 24, 2010 |
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| JDesigner2 | A graphical editor for network models described by biochemical reactions such as signalling, metabolic or gene regulatory networks. | Tool : Network Analysis | Windows, Mac, Linux | June 24, 2010 |
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| Clustal | Multiple alignment of nucleic acid and protein sequences | Tool : Sequence Analysis | Web, Download | June 24, 2010 |
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| Se-Al | Se-Al is an application for creating multiple sequence alignments from nucleotide and amino acid sequences | Tool : Sequence Analysis | Mac | June 24, 2010 |
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| M-coffee | Meta multiple sequence alignment | Tool : Sequence Analysis | Web | June 24, 2010 |
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| T-coffee | T-coffee is a multiple sequence alignment tool | Tool : Sequence Analysis | Web | June 24, 2010 |
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| CoMoDis | Composite Motif Discovery (CoMoDis), which streamlines computational identification of novel regulatory modules | Tool : Gene Regulation | June 24, 2010 |
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| EMMA | EMMA--mouse mutant resources for the international scientific community | Database : Gene Mutant | Web | June 24, 2010 |
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| Molecular Interation Maps | A Molecular Interaction Map (MIM) is a diagram convention that is capable of unambiguous representation of networks containing multi-protein complexes, protein modifications, and enzymes that are substrates of other enzymes | Tool : Interaction | Web | June 24, 2010 |
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| Cytoscape | Platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. | Tool : Interaction | Windows, Mac, Linux, UNIX | June 24, 2010 |
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| REBASE | The Restriction Enzyme Database | Tool : Molecular Biology | Web | June 24, 2010 |
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| pDRAW | pDRAW32 DNA analysis software | Tool : Molecular Biology | Windows, Mac, Linux |