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http://soap.genomics.org.cn/soapsnp.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software providng a method based on Bayes? theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAPsnp (RRID:SCR_010602) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/mira-assembler/wiki/Home/

Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data.

Proper citation: MIRA (RRID:SCR_010731) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/crux/

A software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification. Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra. This software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification is provided as a single executable. Crux is implemented in C and is distributed with source code freely to noncommercial users. Mass spectrometry, the core technology in the field of proteomics, promises to enable scientists to identify and quantify the entire complement of proteins in a complex biological sample. Currently, the primary bottleneck in this type of experiment is computational. Existing algorithms for interpreting mass spectra are slow and fail to identify a large proportion of the given spectra. We describe a database search program called Crux that reimplements and extends the widely used database search program Sequest. For speed, Crux uses a peptide indexing scheme to rapidly retrieve candidate peptides for a given spectrum. For each peptide in the target database, Crux generates shuffled decoy peptides on the fly, providing a good null model and, hence, accurate false discovery rate estimates. Crux also implements two recently described postprocessing methods: a p value calculation based upon fitting a Weibull distribution to the observed scores, and a semisupervised method that learns to discriminate between target and decoy matches. Both methods significantly improve the overall rate of peptide identification.

Proper citation: Crux tandem mass spectrometry analysis software (RRID:SCR_010648) Copy   

•   Source: SciCrunch Registry

http://evexdb.org

EVEX is a text mining resource built on top of PubMed abstracts and PubMed Central full texts. It contains over 40 million bio-molecular events among more than 76 million automatically extracted gene/protein name mentions. The text mining data further has been enriched with gene normalization results, allowing straightforward integration with external resources. Further, gene families from Ensembl and HomoloGene provide homology-based event generalizations. EVEX presents both direct and indirect associations between genes and proteins, enabling explorative browsing of relevant literature.

Proper citation: Evex (RRID:SCR_010509) Copy   

•   Source: SciCrunch Registry

http://snpinfo.niehs.nih.gov/

SNPinfo Web Server is a set of freely available web-based SNP selection tools where investigators can specify genes or linkage regions and select SNPs based on GWAS results, linkage disequilibrium (LD), and predicted functional characteristics of both coding and non-coding SNPs. The algorithm uses GWAS SNP P-value data and finds all SNPs in high LD with GWAS SNPs, so that selection is from a much larger set of SNPs than the GWAS itself. The program can also identify and choose tag SNPs for SNPs not in high LD with any GWAS SNP. We incorporate functional predictions of protein structure, gene regulation, splicing and miRNA binding, and consider whether the alternative alleles of a SNP are likely to have differential effects on function. Users can assign weights for different functional categories of SNPs to further tailor SNP selection. The program accounts for LD structure of different populations so that a GWAS study from one ethnic group can be used to choose SNPs for one or more other ethnic groups. SNP Selection and Functional Information *Candidate Gene SNP Selection (GenePipe):SNP selection for candidate genes based on Genome Wide Association Study (GWAS) results, functional SNP prediction and Linkage Disequilibrium (LD) information. *GWAS Functional SNP Selection (GenomePipe):Functional SNP selection from SNPs that are in high LD with GWAS SNPs *GWAS SNP Selection in Linkage Loci (LinkagePipe):GWAS SNP selection in candidate genomic regions (such as linkage loci) *LD TAG SNP Selection (TagSNP):LD tag SNP selection and visualization for single or multiple populations. Finalization of SNP list from various queries. *SNP Function Prediction (FuncPred): Querying SNP function predictions and ethnic-specific allele frequencies. *SNP Information in DNA Sequence (SNPseq):Visualization of SNP related information in the context of DNA sequence. Preparing DNA Sequence for PCR Primer Design considering SNP information. Detailed information of CpG region.

Proper citation: SNPinfo Web Server (RRID:SCR_010589) Copy   

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http://mirdb.org/miRDB/

An online database for miRNA target prediction and functional annotations.

Proper citation: miRDB (RRID:SCR_010848) Copy   

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http://home.gwu.edu/~wpeng/Software.htm

A clustering software package for identification of enriched domains from histone modification ChIP-Seq data.

Proper citation: SICER (RRID:SCR_010843) Copy   

•   Source: SciCrunch Registry

http://www.netlab.uky.edu/p/bioinfo/MapSplice

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Accurate mapping of RNA-seq reads for splice junction discovery.

Proper citation: MapSplice (RRID:SCR_010844) Copy   

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http://mocklerlab.org/tools/2

A quality-value guided de novo short read assembler.

Proper citation: QSRA (RRID:SCR_010733) Copy   

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http://genetics.cs.ucla.edu/harsh/

Software that provides a method to infer the haplotype using haplotype reference panel and high throughput sequencing data.

Proper citation: HARSH (RRID:SCR_010792) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.jku.at/research/short-IBD/

Software that identifies short identity by descent (IBD) segments that are tagged by rare variants in large sequencing data.

Proper citation: HapFABIA (RRID:SCR_010793) Copy   

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http://www.wageningenur.nl/en/show/Pedimap.htm

A software tool for visualizing phenotypic and genotypic data for related individuals linked in pedigrees.

Proper citation: Pedimap (RRID:SCR_010796) Copy   

•   Source: SciCrunch Registry

http://www.ngsbicocca.org/html/ceqer.html

A graphical, event-driven tool for CNA/AI-coupled analysis of exome sequencing reads.

Proper citation: CEQer (RRID:SCR_010813) Copy   

•   Source: SciCrunch Registry

http://bg.upf.edu/group/projects/oncodrive-fm.php

An approach to uncover driver genes or gene modules.

Proper citation: Oncodrive-fm (RRID:SCR_010781) Copy   

•   Source: SciCrunch Registry

http://www.bcgsc.ca/platform/bioinfo/software/ssake

Software designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets.

Proper citation: SSAKE (RRID:SCR_010753) Copy   

•   Source: SciCrunch Registry

http://www.embl.de/~korbel/CopySeq/

A computational tool that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can integrate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes.

Proper citation: CopySeq (RRID:SCR_010758) Copy   

•   Source: SciCrunch Registry

https://github.com/ekg/freebayes

A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment.

Proper citation: FreeBayes (RRID:SCR_010761) Copy   

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http://www.uhnresearch.ca/labs/tillier/ProDesign/ProDesign.html

Webserver that can be used to find oligonucleotide probe sets for microarray slides. The probes can be for individual sequences or for clusters of genes. This webserver accepts files up to 200 kb in size in order to minimize the running time. For larger files please download the program.

Proper citation: ProDesign (RRID:SCR_010966) Copy   

•   Source: SciCrunch Registry

http://bioinfo-out.curie.fr/projects/micsa/

A software package for the identification of transcription factor binding sites in ChIP-Seq data, developed by Computational Systems Biology of Cancer group at the Bioinformatics Laboratory of Institut Curie (Paris).

Proper citation: MICSA (RRID:SCR_010860) Copy   

•   Source: SciCrunch Registry

http://www.cs.ucr.edu/~polishka/

A command line software tool for accurate placing of the nucleosomes using a Modified Gaussian Mixture Model. It was designed to resolve overlapping nucleosomes and extract extra information (fuzziness, probability, etc.) of nucleosome placement. To achieve this goal the tool clusters the input tags according to Nucleosome Model (see the paper for detailed description) using EM learning process. The tool is written in C++. There are no special requirements except for g++ compiler and *nix environment to compile and use the tool. It was checked to compile using g++ compiler under Ubuntu 11.04 and Mac OS X 10.6

Proper citation: NOrMAL (RRID:SCR_010889) Copy   

•   Source: SciCrunch Registry