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http://microbiology.se/software/megraft/
A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes.
Proper citation: Megraft (RRID:SCR_000240) Copy
http://compbio.cs.utoronto.ca/varid/
Software using a Hidden Markov Model for SNP (single nucleotide polymorphism) and indel identification with AB-SOLiD color-space as well as regular letter-space reads.
Proper citation: VARiD (RRID:SCR_000241) Copy
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://www.tripos.com/index.php?family=modules,SimplePage,surflex_dock
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software program that screens large libraries of compounds including ligands, and their docking.
Proper citation: Surflex-Dock (RRID:SCR_000196) Copy
https://cran.r-project.org/src/contrib/Archive/MetaDE/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. Software package that implements 12 major meta-analysis methods for differential expression analysis.Package was removed from the CRAN repository.Formerly available versions can be obtained from the archive.Archived on 2018-01-23 as check problems were not corrected in time.
Proper citation: MetaDE (RRID:SCR_000199) 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://www.scfbio-iitd.res.in/sanjeevini/sanjeevini.jsp
A complete drug designing software suite with an accessible web-server for targeted directed lead molecule discovery.
Proper citation: Sanjeevini (RRID:SCR_000191) Copy
http://exon.gatech.edu/paul/unsplicer/index.htm
An RNA-seq alignment program that provides alignment of short reads to a reference genome. The program requires two inputs that are provided by the output of GeneMark-ES: HMM model parameters and ab initio gene predictions. UnSplicer is a sister pipeline to TrueSight.
Proper citation: UnSplicer (RRID:SCR_000226) Copy
https://github.com/matteocereda/RNAmotifs
Software that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs.
Proper citation: RNAmotifs (RRID:SCR_000263) 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://bioinfo5.ugr.es/miRanalyzer/miRanalyzer.php
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. A microRNA detection and analysis tool for next-generation sequencing experiments. The program uses a minimum match length of 17bp starting at the first base of the read. The maximum read length is set to 28bp. Reads with more than 5 matches to the genome are discarded, and if a read matches to more than 5 transcripts or Rfam entries it will be removed.
Proper citation: miRanalyzer (RRID:SCR_000163) Copy
http://www.dnastar.com/t-seqmanpro.aspx
Software for analysis and DNA sequence assembly of Sanger data. It also provides visualizations and analysis of next-gen projects assembled by SeqMan NGen.
Proper citation: Lasergene's SeqMan Pro (RRID:SCR_000283) 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://sourceforge.net/projects/omssapercolator/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software tool which interfaces OMSSA with Percolator, a post search machine learning method for rescoring database search results.
Proper citation: OMSSAPercolator (RRID:SCR_000287) Copy
http://www.bioconductor.org/packages/devel/bioc/html/CNTools.html
Software package that provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data.
Proper citation: CNTools (RRID:SCR_000281) Copy
A freely available complete software platform for comprehensive and integrated analysis and visualization of large proteomics datasets.
Proper citation: GProX (RRID:SCR_000273) 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
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