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http://www.broadinstitute.org/gsea/
Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.
Proper citation: Gene Set Enrichment Analysis (RRID:SCR_003199) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2023. A simple tab-delimited, spreadsheet-based format which will become a part of the MAGE microarray data standard that can be used for annotating and communicating microarray data in a MIAME compliant fashion. MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML.
Proper citation: MAGE-TAB (RRID:SCR_003222) Copy
http://creskolab.uoregon.edu/stacks/
A software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. It was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
Proper citation: Stacks (RRID:SCR_003184) Copy
http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/
Software tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e., the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.
Proper citation: RNAhybrid (RRID:SCR_003252) Copy
Computational biology resource for investigating candidate functional sites in eukarytic proteins. Functional sites which fit to the description linear motif are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives. The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive.
Proper citation: Eukaryotic Linear Motif (RRID:SCR_003085) Copy
An open source JavaScript library of components for visualisation of biological data on the web.
Proper citation: BioJS (RRID:SCR_003119) Copy
Central online repository for microRNA nomenclature, sequence data, annotation and target prediction.Collection of published miRNA sequences and annotation.
Proper citation: miRBase (RRID:SCR_003152) Copy
A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request.
Proper citation: QGene (RRID:SCR_003209) Copy
https://planttfdb.gao-lab.org/
Comprehensive plant transcription factor database. Interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors
Proper citation: PLANTTFDB (RRID:SCR_003362) Copy
https://bioconductor.org/packages/genomation/
Software R package for simplfiying common tasks in genomic feature analysis. Toolkit to summarize, annotate and visualize genomic intervals. Provides functions for reading BED and GFF files as GRanges objects, summarizing genomic features over predefined windows so users can make average enrichment of features over defined regions or produce heatmaps. Can annotate given regions with other genomic features such as exons,introns and promoters.
Proper citation: genomation (RRID:SCR_003435) Copy
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/
Software R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Weighted Gene Co-expression Network Analysis (RRID:SCR_003302) Copy
Data collection for Xenopus laevis and Xenopus tropicalis biology and genomics.
Proper citation: Xenbase (RRID:SCR_003280) Copy
Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures.
Proper citation: SMART (RRID:SCR_005026) Copy
A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage cornerstone feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage quality and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. Databases available for download include Virus DB, Prophage and virus DB, Bacteria DB, and PHAST result DB. Pre-calculated genomes for viewing are also available.
Proper citation: PHAge Search Tool (RRID:SCR_005184) Copy
http://ccb.jhu.edu/software/FLASH/
Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data.
Proper citation: FLASH (RRID:SCR_005531) Copy
https://github.com/mfumagalli/ngsTools
A collection of software programs for population genetics analyses from NGS (Next-Generation Sequencing) data, taking into account its statistical uncertainty. The methods implemented in these programs do not rely on SNP (Single Nucleotide Polymorphism) or genotype calling, and are particularly suitable for low sequencing depth data.
Proper citation: ngsTools (RRID:SCR_005489) Copy
http://solexaqa.sourceforge.net/
Software package to calculate sequence quality statistics and create visual representations of data quality for Illumina's second-generation sequencing technology.
Proper citation: SolexaQA (RRID:SCR_005421) Copy
A web-based software package for comparative genomics.
Proper citation: Sybil (RRID:SCR_005593) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets.
Proper citation: CLIPZ (RRID:SCR_005755) Copy
Free access to biomedical literature resources including all of PubMed and PubMed Central, agricultural abstracts (from AGRICOLA), over 4 million international life science patents abstracts, National Health Service (NHS) clinical guidelines, and is supplemented with Chinese Biological Abstracts and the Citeseer database. As well as powerful search of abstracts and full text articles, it also includes: * article citations and sort order based on citation count * data citations mined from full text articles * links to and from related databases and institutional repositories * a tool to create bibliographies linked to your ORCID * named entity recognition of keywords and text-mining-based applications showcased in Europe PMC Labs * Tools for recipients of grants from one of the Europe PMC funders to deposit full-text manuscripts and link them to those specific grants. * Web services for programmatic access to all the above bibliographic information and 50,000 grants. * Search by publication date, relevance, or the number of times an article has been cited. * Links to public databases such as UniProt, Protein Data Bank (PDBe), and the European Nucleotide Archive (ENA) are provided. * Through textmining technologies, you can highlight and browse keywords such as gene names, organisms and diseases. * Search 40,000 biomedical research grants awarded to the 18,000 PIs supported by the Europe PMC funders. * Roadtest new tools based on Europe PMC content in Europe PMC labs. * In Europe PMC plus, PIs supported by the Europe PMC funders can link grants to publication information, view article citation and download statistics, and submit manuscripts.
Proper citation: Europe PubMed Central (RRID:SCR_005901) Copy
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