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http://iresite.org/

Database of experimentally verified IRES structures. Presents information about experimentally studied Internal Ribosome Entry Site segments.

Proper citation: IRESite (RRID:SCR_007753) Copy   

•   Source: SciCrunch Registry

http://gump.qimr.edu.au/general/daleN/SNPSpD/

SNPSpD is a method of correcting for non-independance of single nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of LD between SNP''s. Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor loadings after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region.

Proper citation: Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) (RRID:SCR_008621) Copy   

•   Source: SciCrunch Registry

http://wwwmgs.bionet.nsc.ru/mgs/programs/panalyst/

WebProAnalyst provides web-accessible analysis for scanning the quantitative structure-activity relationships in protein families. It searches for a sequence region, whose substitutions are correlated with variations in the activities of a homologous protein set, the so-called activity modulating sites. WebProAnalyst allows users to search for the key physicochemical characteristics of the sites that affect the changes in protein activities. It enables the building of multiple linear regression and neural networks models that relate these characteristics to protein activities. WebProAnalyst implements multiple linear regression analysis, back propagation neural networks and the Structure-Activity Correlation/Determination Coefficient (SACC/SADC). A back propagation neural network is implemented as a two-layered network, one layer as input, the other as output (Rumelhart et al, 1986). WebProAnalyst uses alignment of amino acid sequences and data on protein activity (pK, Km, ED50, among others). The input data are the numerical values for the physicochemical characteristics of a site in the multiple alignment given by a slide window. The output data are the predicted activity values. The current version of WebProAnalyst handles a single activity for a single protein. The SACC/SADC may be defined as an estimate of the strongest multiple correlation between the physicochemical characteristics of a site in a multiple alignment and protein activities. The SACC/SADC coefficient makes possible the calculation of the possible highest correlation achievable for the quantitative relationship between the physicochemical properties of sites and protein activities. The SACC/SADC is a convenient means for an arrangement of positions by their functional significance. WebProAnalyst outputs a list of multiple alignment positions, the respective correlation values, also regression analysis parameters for the relationships between the amino acid physicochemical characteristics at these positions and the protein activity values.

Proper citation: Webproanalyst (RRID:SCR_008348) Copy   

•   Source: SciCrunch Registry

http://www.cs.tau.ac.il/~spike/

Database of curated human signaling pathways with an associated interactive software tool for analysis and dynamic visualization of pathways. Individual pathway maps can be viewed and downloaded; the entire database may be browsed, or launched via a map viewer tool that allows dynamic visualization of the database and save networks in XGMML format that can be viewed in all generic XGMML viewers. Map Topics * Cell cycle progress and check points * DNA damage response * Programmed cell death related processes * Stress-activated transcription factors * Mitogen-activated protein kinase pathways * Immune response signaling * HEarSpike: hearing related pathways

Proper citation: SPIKE (RRID:SCR_010466) Copy   

•   Source: SciCrunch Registry

http://tools.neb.com/NEBcutter2/

This tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once. By default, only enzymes available from NEB are used, but other sets may be chosen. Just enter your sequence and submit. Further options will appear with the output. The maximum size of the input file is 1 MByte, and the maximum sequence length is 300 KBases. NEBcutter produces a variety of outputs including restriction enzyme maps, theoretical digests and links into the restriction enzyme database, REBASE (http://rebase.neb.com/rebase/rebase.html). Importantly, its table of recognition sites is updated daily from REBASE and it marks all sites that are potentially affected by DNA methylation (Dam, Dcm, etc.). Many options exist to choose the enzymes used for digestion, including all known specificities, subsets of those that are commercially available or sets of enzymes that produce compatible termini.

Proper citation: NEBcutter (RRID:SCR_010664) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.mutationtaster.org/

Evaluates disease-causing potential of sequence alterations.

Proper citation: MutationTaster (RRID:SCR_010777) Copy   

•   Source: SciCrunch Registry

http://www.benoslab.pitt.edu/comir/

Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data.

Proper citation: ComiR (RRID:SCR_013023) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/EGSEA/

Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets.

Proper citation: EGSEA (RRID:SCR_015036) Copy   

•   Source: SciCrunch Registry

http://www.genoread.org/

A sequence verification pipeline where users can submit trace files to verify if a clone''s physical sequence matches its reference sequence.

Proper citation: GenoREAD (RRID:SCR_012007) Copy   

•   Source: SciCrunch Registry

http://zope.bioinfo.cnio.es/plan2l/plan2l.html

A web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. The system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned.

Proper citation: PLAN2L (RRID:SCR_013346) Copy   

•   Source: SciCrunch Registry

http://dsap.cgu.edu.tw/

A web server designed to provide a total solution to analyze small RNAs sequencing data generated by SOLEXA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DSAP (RRID:SCR_013352) Copy   

•   Source: SciCrunch Registry

https://www.hmtvar.uniba.it

Manually curated database offering variability and pathogenicity information about mtDNA variants. Human mitochondrial variants data of healthy and diseased subjects.Data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information.

Proper citation: HmtVar (RRID:SCR_017288) Copy   

•   Source: SciCrunch Registry

http://www.gramene.org

Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site.

Proper citation: Gramene (RRID:SCR_002829) Copy   

•   Source: SciCrunch Registry

http://pfind.ict.ac.cn/software/pNovo/index.html

A de novo peptide sequencing algorithm using complementary higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD) tandem mass spectra.

Proper citation: pNovo+ (RRID:SCR_002860) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/pairheatmap/

A software tool to compare two heatmaps and discover patterns within and across groups. In the context of biology, group can be defined based on gene ontology.

Proper citation: pairheatmap (RRID:SCR_003109) Copy   

•   Source: SciCrunch Registry

https://github.com/quwubin/MFEprimer/

A fast thermodynamics-based software program for checking PCR primer specificity against genomic DNA and mRNA/cDNA sequence databases.

Proper citation: MFEprimer (RRID:SCR_003066) Copy   

•   Source: SciCrunch Registry

https://github.com/timflutre/eqtlbma/wiki

Software package that implements Bayesian statistical methods to detect eQTLs jointly in multiple subgroups (e.g. tissues). Key features are to borrow information across subgroups, to explicitly model heterogeneity (qualitatively and quantitatively), and to borrow information across genes to estimate hyper-parameters from the data (empirical Bayes).

Proper citation: eQtlBma (RRID:SCR_003102) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/triplex.html

Software package that provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many canonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.

Proper citation: Triplex (RRID:SCR_003061) Copy   

•   Source: SciCrunch Registry

https://github.com/CRG-Barcelona/bwtool/wiki

A command-line utility for bigWig files designed to read bigWig files rapidly and efficiently, providing functionality for extracting data and summarizing it in several ways, globally or at specific regions. Its functionality is subdivided into subprograms that roughly fall into three categories: data extraction, analysis, and data modification, although e.g. in the case of the matrix program or the sax program, the boundary between data extraction and analysis isn't very strong. The data modification programs all have the behavior that a bigWig is inputted and a new bigWig is outputted.

Proper citation: bwtool (RRID:SCR_003035) Copy   

•   Source: SciCrunch Registry