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https://github.com/eduardporta/e-Driver

Software tool to identify cancer driver genes based on linear annotations of biological regions such as protein domains.Uses information on three-dimensional structures of mutated proteins to identify specific structural features. Then algorithm analyzes whether these features are enriched in cancer somatic mutations and are candidate driver genes.

Proper citation: e-Driver (RRID:SCR_002674) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/igblast/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 4,2023. IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin V region sequences in GenBank. In addition to performing a regular BLAST search, IgBLAST has several additional functions: - Reports the germline V, D and J gene matches to the query sequence. - Annotates the immunoglobulin domains (FWR1 through FWR3). - Matches the returned hits (for databases other than germline genes) to the closest germline V genes, making it easier to identify related sequences. - Reveals the V(D)J junction details such as nucleotide homology between the ends of V(D)J segments and N nucleotide insertions. D and J gene reporting is only for nucleotide sequence search and requires a stretch of five or more nucleotide identity between the query and D or J genes. Sponsors: This resource is supported by the National Center for Biotechnology Information, a division of the U.S. National Library of Medicine.

Proper citation: IgBLAST (RRID:SCR_002873) Copy   

•   Source: SciCrunch Registry

http://systemsbio.ucsd.edu/GoSurfer/

GoSurfer uses Gene Ontology (GO) information to analyze gene sets obtained from genome-wide computations or microarray analyses. GoSurfer is a graphical interactive data mining tool. It associates user input genes with GO terms and visualizes such GO terms as a hierarchical tree. Users can manipulate the tree output by various means, like setting heuristic thresholds or using statistical tests. Significantly important GO terms resulted from a statistical test can be highlighted. All related information are exportable either as texts or as graphics. Platform: Windows compatible

Proper citation: GoSurfer (RRID:SCR_005789) Copy   

•   Source: SciCrunch Registry

http://www.bioinfo.no/tools/bomp

BOMP is a tool for prediction of beta-barrel integral outer membrane proteins. The user may submit a list of proteins, and receive a list of predicted BOMPs. The program, called the beta-barrel Outer Membrane protein Predictor (BOMP), is based on two separate components to recognize integral beta-barrel proteins. The first component is a C-terminal pattern typical of many integral beta-barrel proteins. The second component calculates an integral beta-barrel score of the sequence based on the extent to which the sequence contains stretches of amino acids typical of transmembrane -strands. To use the BOMP tool simply paste your fasta-formatted sequences into the text area, or choose a file which contains sequences. Then hit the submit button. It is possible to perform a BLAST search parallel with the predictions, which may be suitable in some cases. Using the BLAST search will however increase the running time substantially. Sponsors: This work was supported in part by grants from the Norwegian Research Council [SUP 140785/420 (GABI); FUGE/CBU151899/ISO], and the Meltzer Foundation, University of Bergen. Keywords: Beta-barrel, Membrane, Protein, Program, Software, Beta strand, Bacteria,

Proper citation: BOMP: beta-barrel Outer Membrane protein Predictor (RRID:SCR_007268) Copy   

•   Source: SciCrunch Registry

https://varscan.sourceforge.net/

Platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples. (entry from Genetic Analysis Software).

Proper citation: VarScan (RRID:SCR_006849) Copy   

•   Source: SciCrunch Registry

http://zfishbook.org/

Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates.

Proper citation: zfishbook (RRID:SCR_006896) Copy   

•   Source: SciCrunch Registry

http://droog.gs.washington.edu/ldSelect.html

Software program that analyzes patterns of linkage disequilibrium (LD) between polymorphic sites in a locus, and bins the SNPs on the basis of a threshold level of LD as measured by r2. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LDSELECT (RRID:SCR_007010) Copy   

•   Source: SciCrunch Registry

http://watson.hgen.pitt.edu/register/soft_doc.html

Software application that is a faster version of SLINK (entry from Genetic Analysis Software)

Proper citation: FASTSLINK (RRID:SCR_008664) Copy   

•   Source: SciCrunch Registry

http://mga.bionet.nsc.ru/soft/pedpeel/

Software program that prepares pedigree data for calculation of Elston-Stewarts'' likelihood function. It finds an optimal way to peel a pedigree and returns text file containing 7 description arrays (entry from Genetic Analysis Software)

Proper citation: PEDPEEL (RRID:SCR_008436) Copy   

•   Source: SciCrunch Registry

http://www.homepages.ed.ac.uk/pmckeigu/admixmap/index.html

General-purpose program for modelling admixture, using marker genotypes and trait data on a sample of individuals from an admixed population (such as African-Americans), where the markers have been chosen to have extreme differentials in allele frequencies between two or more of the ancestral populations between which admixture has occurred. The main difference between ADMIXMAP and classical programs for estimation of admixture such as ADMIX is that ADMIXMAP is based on a multilevel model for the distribution of individual admixture in the population and the stochastic variation of ancestry on hybrid chromosomes. This makes it possible to model the associations of ancestry between linked marker loci, and the association of a trait with individual admixture or with ancestry at a linked marker locus. (entry from Genetic Analysis Software)

Proper citation: ADMIXMAP (RRID:SCR_009035) Copy   

•   Source: SciCrunch Registry

http://mga.bionet.nsc.ru/soft/index.html

Software application that allows drawing pedigrees with a difficult structure, those containing consanguinity loops, and those individuals with multiple mates or several related families (entry from Genetic Analysis Software)

Proper citation: PEDIGREEQUERY (RRID:SCR_009041) Copy   

•   Source: SciCrunch Registry

https://github.com/gaow/genetic-analysis-software/blob/master/pages/MOSCPHASER.md

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software application for inferring haplotypes composed of both CNV alleles and SNP alleles.

Proper citation: MOSCPHASER (RRID:SCR_009092) Copy   

•   Source: SciCrunch Registry

http://tcoffee.crg.cat/apps/tcoffee/do:regular

A multiple sequence alignment server which can align Protein, DNA and RNA sequences.

Proper citation: T-Coffee (RRID:SCR_011818) Copy   

•   Source: SciCrunch Registry

http://probcons.stanford.edu/

Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.

Proper citation: ProbCons (RRID:SCR_011813) Copy   

•   Source: SciCrunch Registry

http://plantgrn.noble.org/psRNATarget/

A plant small RNA target analysis server which features two important analysis functions: 1) reverse complementary matching between miRNA and target transcript using a proven scoring schema, and 2) target site accessibility evaluation by calculating unpaired energy (UPE) required to ?open? secondary structure around miRNA?s target site on mRNA. PsRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of miRNA/target site pairs that may affect miRNA binding activity to target transcript. PsRNATarget is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster. The server front-end integrates three simplified user-friendly interfaces to accept user-submitted or preloaded miRNAs and transcript sequences; and outputs a comprehensive list of miRNA / target pairs along with the online tools for batch downloading, key word searching and results sorting., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: psRNATarget (RRID:SCR_013321) Copy   

•   Source: SciCrunch Registry

http://nhjy.hzau.edu.cn/kech/swxxx/jakj/dianzi/Bioinf6/GeneFinding/GeneFinding2.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 10,2020. Data analysis service for Hidden Markov Model (HMM)-based gene structure prediction (multiple genes, both chains).

Proper citation: FGENESH (RRID:SCR_011928) Copy   

•   Source: SciCrunch Registry

http://race.unil.ch/

A collection of web tools designed to assist with the analysis of DNA microarray data and results. RACE performs probe level data preprocessing, quality checks, normalization, and visualization for Affymetrix GeneChips. In addition, it performs clustering and differential analysis of normalized expression levels or ratios for arbitrary platforms, and estimates the false discovery rates in lists of potentially regulated genes. A Gene Ontology (GO)-term analysis assists in the biological interpretation of gene lists. The user can customize each analysis request; upon submission the analysis is executed in a fully automated way., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RACE (RRID:SCR_010950) Copy   

•   Source: SciCrunch Registry

http://www.imtech.res.in/raghava/hslpred/

A support vector machine (SVM)-based method for the prediction of 4 major subcellular localization (cytoplasm, mitochondrial, nuclear and plasma membrane) of human proteins using various features such as i) amino acid composition, ii) dipeptide composition and iii) evolutionary information of proteins.

Proper citation: HSLPred (RRID:SCR_011972) Copy   

•   Source: SciCrunch Registry

http://159.149.160.51/pscan_chip_dev/

Web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria.

Proper citation: Pscan-ChIP (RRID:SCR_010885) Copy   

•   Source: SciCrunch Registry

http://genes.mit.edu/GENSCAN.html

Web server for identification of complete gene structures in genomic DNA.Tool for predicting locations and exon-intron structures of genes in genomic sequences from variety of organisms. Used for prediction of complete gene structures in human genomic DNA.

Proper citation: GENSCAN (RRID:SCR_013362) Copy   

•   Source: SciCrunch Registry