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http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
Software designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
Proper citation: BLAT (RRID:SCR_011919) Copy
http://www.bios.unc.edu/research/genomic_software/BBSeq/
A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data.
Proper citation: BBSeq (RRID:SCR_011877) Copy
Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events.
Proper citation: KisSplice (RRID:SCR_011893) Copy
http://uc-echo.sourceforge.net/
Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II.
Proper citation: ECHO (RRID:SCR_011851) Copy
http://bioinformatics.mdanderson.org/main/PRADA:Overview
A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates.
Proper citation: PRADA (RRID:SCR_011906) Copy
https://mcdonaldlab.biology.gatech.edu/r-sap/
An automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets.
Proper citation: R-SAP (RRID:SCR_011907) Copy
Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species.
Proper citation: JiffyNet (RRID:SCR_011954) Copy
http://www.optimaldesign.com/ArrayMiner/ArrayMiner.htm
A set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data.
Proper citation: ArrayMiner (RRID:SCR_011955) Copy
http://sourceforge.net/projects/mirplant/
A user-friendly plant miRNA prediction tool.
Proper citation: miRPlant (RRID:SCR_012105) Copy
https://code.google.com/p/slidesort-bpr/
Software using a reference-free method for detecting clusters of breakpoints from the chromosomal rearrangements.
Proper citation: SlideSort-BPR (RRID:SCR_012079) Copy
http://www.bioinf.jku.at/software/fabia/fabia.html
A model-based technique for biclustering that is clustering rows and columns simultaneously.
Proper citation: FABIA (RRID:SCR_012002) Copy
Software that allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison).
Proper citation: MFPaQ (RRID:SCR_012049) Copy
http://sourceforge.net/projects/multiplierz/
An open-source Python-based environment that provides a scriptable framework for efficient access to manufacturers'' proprietary data files via mzAPI.
Proper citation: multiplierz (RRID:SCR_012058) Copy
http://www.computationalbioenergy.org/meta-storms.html
Optimized GPU-based software to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples.
Proper citation: GPU-Meta-Storms (RRID:SCR_012029) Copy
http://opencobra.sourceforge.net/openCOBRA/Welcome.html
Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods.
Proper citation: COBRApy (RRID:SCR_012096) Copy
https://code.google.com/p/netcoffee/
A fast and accurate algorithm which allows to find a global alignment of multiple protein-protein interaction networks.
Proper citation: NetCoffee (RRID:SCR_012095) Copy
A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences.
Proper citation: cpnDB: A Chaperonin Database (RRID:SCR_002263) Copy
http://www.predictprotein.org/
Web application for sequence analysis and the prediction of protein structure and function. The user interface intakes protein sequences or alignments and returned multiple sequence alignments, motifs, and nuclear localization signals., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.
Proper citation: Predictions for Entire Proteomes (RRID:SCR_002803) Copy
Database on transcriptional regulation in Escherichia coli K-12 containing knowledge manually curated from original scientific publications, complemented with high throughput datasets and comprehensive computational predictions. Graphic and text-integrated environment with friendly navigation where regulatory information is always at hand. They provide integrated views to understand as well as organized knowledge in computable form. Users may submit data to make it publicly available.
Proper citation: RegulonDB (RRID:SCR_003499) Copy
Software package for Bayesian analysis of protein, DNA and RNA sequences. It utilizes multiple alignments, phylogenetic trees and evolutionary parameters to quantify uncertainty in these analyses. It is written in Java.
Proper citation: StatAlign (RRID:SCR_001892) Copy
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