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Web based integrative platform for transcriptional regulation studies.
Proper citation: Cistrome (RRID:SCR_000242) Copy
http://bioinformatics.psb.ugent.be/webtools/tapir/
Web server designed for prediction of plant microRNA targets.
Proper citation: TAPIR: target prediction for plant microRNAs (RRID:SCR_000237) Copy
http://iclab.life.nctu.edu.tw/iclab_webtools/sodock/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems.
Proper citation: SODOCK (RRID:SCR_000193) Copy
http://sourceforge.net/projects/protms/
A software tool for the proteomics community that may help improving analysis of proteomic experimental data.
Proper citation: Quant (RRID:SCR_000267) Copy
http://open2dprot.sourceforge.net/Flicker/
An open-source stand-alone computer program for visually comparing 2D gel images.
Proper citation: Flicker (RRID:SCR_000288) Copy
http://sourceforge.net/projects/biogrinder/
An open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. The tool is available through multiple interfaces like GUI, CLI and API. It is useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities.
Proper citation: Grinder (RRID:SCR_000168) Copy
http://www.bioconductor.org/packages/release/bioc/html/cn.farms.html
Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff.
Proper citation: cn.FARMS (RRID:SCR_000289) Copy
http://peptideprophet.sourceforge.net/
Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST.
Proper citation: PeptideProphet (RRID:SCR_000274) Copy
http://www.cs.toronto.edu/~hilal/rnacontext/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Motif finding software suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RNA-binding proteins (RBPs) for a wide range of RNA sequences and structures. The tool is also implemented in a website.
Proper citation: RNAcontext (RRID:SCR_000179) Copy
http://cakesomatic.sourceforge.net/
A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone.
Proper citation: Cake (RRID:SCR_002133) Copy
http://www.yandell-lab.org/software/vaast.html
A probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST combines elements of phylogenetic conservation, amino acid substitution, and aggregative approaches to variant prioritization into a single unified likelihood-framework that allows users to accurately identify damaged genes and deleterious variants. The software can score both coding (SNV, indel and splice site) and non-coding variants (SNV), evaluating the cumulative impact of both types of variants simultaneously. It can identify rare variants causing rare genetic diseases and can also use both rare and common variants to identify genes responsible for common diseases.
Proper citation: VAAST (RRID:SCR_002179) Copy
Portal providing access to all JGI genomic databases and analytical tools, sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web.
Proper citation: JGI Genome Portal (RRID:SCR_002383) Copy
https://github.com/mpyatkov/sbars
Bioinformatics tool for searching different types of long repeats in sequences comparable by size with chromosomes.
Proper citation: SBARS (RRID:SCR_002371) Copy
http://www.bioconductor.org/packages/release/bioc/html/CAMERA.html
A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data.
Proper citation: CAMERA - Collection of annotation related methods for mass spectrometry data (RRID:SCR_002466) Copy
Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
Proper citation: Ensembl (RRID:SCR_002344) Copy
http://www.ncbi.nlm.nih.gov/SNP/
General database of genetic variations maintained by the NCBI. Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource.
Proper citation: dbSNP (RRID:SCR_002338) Copy
http://droog.gs.washington.edu/polyphred/
Software program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. Its functions are integrated with the use of three other programs: Phred (Brent Ewing and Phil Green), Phrap (Phil Green), and Consed (David Gordon and Phil Green). PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool.
Proper citation: PolyPhred (RRID:SCR_002337) Copy
http://cran.r-project.org/web/packages/isa2/
A biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix.
Proper citation: Iterative Signature Algorithm (RRID:SCR_002327) Copy
http://kirchnerlab.github.io/libmgf/
A flex/bison-based C++ Mascot Generic Format (MGF) parser library.
Proper citation: libmgf (RRID:SCR_002664) Copy
http://cran.r-project.org/web/packages/ExomeDepth/
Software that calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
Proper citation: ExomeDepth (RRID:SCR_002663) Copy
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