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A targeting model that defines where mutations occur (by specifying the relative rates at which DNA motifs in the Ig sequence are mutated), and a nucleotide substitution model that defines the resulting mutation (by specifying the probability of each base mutating to each of the other three possibilities as a function of the surrounding bases).
Proper citation: Models of SHM Targeting and Substitution (RRID:SCR_005250) Copy
https://cab.spbu.ru/software/spades/
Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SPAdes (RRID:SCR_000131) Copy
A software infrastructure, course and tool set for teaching bioinformatics, and biology through the use of models. This platform for learning bioinformatics through problem solving aims to make learning bioinformatics fun and easy. Learning bioinformatics usually requires solving computational problems of varying difficulty that are extracted from real challenges of molecular biology. Rosalind offers an array of intellectually stimulating problems that grow in biological and computational complexity; each problem is checked automatically, so that the only resource required to learn bioinformatics is an internet connection. Rosalind also promises to facilitate improvements in standard bioinformatics education by providing a vital teaching aid and a central homework resource. Rosalind is inspired by Project Euler, Google Code Jam, and the ever growing movement of free online courses. The project''s name commemorates Rosalind Franklin, whose X-ray crystallography with Raymond Gosling facilitated the discovery of the DNA double helix by Watson and Crick. We hope that Rosalind will inspire a new generation of bioinformatics students by attracting biologists who want to develop vital programming skills at their own pace in a unique environment as well as programmers who have never been exposed to some of the stimulating computational problems generated by molecular biology.
Proper citation: Rosalind (RRID:SCR_006233) Copy
http://www.koada.com/koadarray/
A fully automatic array image analysis software which can process single or multiple array images. Koadarray automatically finds the spot locations within each image and quantifies the spot intensity data. It can be used in conjunction with radioactive applications, macroarray applications, fluorescent microarray image analysis and fluorescent microplate images.
Proper citation: Koadarray (RRID:SCR_000321) Copy
http://cran.r-project.org/web/packages/CpGassoc/index.html
Software R package to test association between methylation at CpG sites across genome and phenotype of interest, adjusting for any relevant covariates. Can perform standard analyses of large datasets without need to manually input data. Can handle mixed effects models with chip or batch entering model as random intercept. Includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.
Proper citation: CpGassoc (RRID:SCR_000320) Copy
Database to explore known and predicted interactions of chemicals and proteins. It integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. The database contains interaction information for over 68,000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database.
Proper citation: Search Tool for Interactions of Chemicals (RRID:SCR_007947) Copy
Database that provides access to mRNA sequences and associated regulatory elements that were processed from Genbank. These mRNA sequences include complete genomes, which are divided into 5-prime UTRs, 3-prime UTRs, initiation sequences, termination regions and full CDS sequences. This data can be searched for a range of properties including specific mRNA sequences, mRNA motifs, codon usage, RSCU values, information content, etc.
Proper citation: Transterm (RRID:SCR_008244) Copy
http://omicsomics.blogspot.fr/
A computational biologist''s personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery.
Proper citation: OMICS! OMICS! (RRID:SCR_008533) Copy
Service that allows you to process CEL files from Affymetrix, Inc. GeneChip Exon 1.0 ST Arrays to identify alternative splicing.
Proper citation: Exon Array Analyzer (RRID:SCR_008684) Copy
We share commentaries, news and announcement that advance our goal of helping clinical labs to adopt next generation sequencing for the analysis of diagnostic gene targets.
Proper citation: Omixon blog (RRID:SCR_010020) Copy
http://mcg.ustc.edu.cn/sdap1/cpss/index.html
Computational Platform for analysis of Small RNA deep Sequencing data BioStaCs group., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CPSS (RRID:SCR_009395) Copy
http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index
Manually curated database of experimentally supported animal microRNA targets. Collection of experimentally supported miRNA gene interactions.
Proper citation: TarBase (RRID:SCR_010841) Copy
A website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis.
Proper citation: SNPs3D (RRID:SCR_010787) Copy
http://tools.genxpro.net/omiras/
A web server for the annotation, comparison and visualization of interaction networks of non-coding RNAs derived from small RNA-Sequencing experiments of two different conditions.
Proper citation: omiRas (RRID:SCR_010833) Copy
http://compbio.med.harvard.edu/CGHweb/
Data analysis service enabling users to analyse their array-CGH data with multiple algorithms simultaneously.
Proper citation: CGHweb (RRID:SCR_010923) Copy
http://agvgd.iarc.fr/index.php
A freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral.
Proper citation: Align-GVGD (RRID:SCR_010772) Copy
http://cosmoss.org/bm/plantapdb
A phylogeny-based comprehensive database of plant transcription associated proteins.
Proper citation: PlanTAPDB (RRID:SCR_010897) Copy
http://www.mutationtaster.org/
Evaluates disease-causing potential of sequence alterations.
Proper citation: MutationTaster (RRID:SCR_010777) Copy
http://hyperbrowser.uio.no/hb/
A generic web-based system, providing statistical methodology and computing power to handle a variety of biological inquires on genomic datasets.
Proper citation: Genomic HyperBrowser (RRID:SCR_010909) Copy
https://genome-cancer.ucsc.edu/
A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets.
Proper citation: UCSC Cancer Genomics Browser (RRID:SCR_011796) Copy
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