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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Webproanalyst Resource Report Resource Website |
Webproanalyst (RRID:SCR_008348) | service resource, analysis service resource, data analysis service, production service resource | 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. | family, functional, activity, alignment, amino acid, homologous, modulating site, neural, physicochemical, propagation, protein, quantitative, region, relationship, scan, sequence, structure, substitution, variation, bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-25212, biotools:webproanalyst | https://bio.tools/webproanalyst | SCR_008348 | Webproanalyst | 2026-02-15 09:19:47 | 0 | ||||||||
|
SPIKE Resource Report Resource Website 100+ mentions |
SPIKE (RRID:SCR_010466) | SPIKE | data or information resource, database, service resource | 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 | visualization, analysis, cellular, signaling pathway, regulatory network, function, genomic, proteomic, cell cycle, dna damage, cell death, stress, transcription factor, mitogen, protein kinase, pathway, immune response, signaling, hearing, dna damage response, programmed cell death, development, ear, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: ConsensusPathDB has parent organization: Tel Aviv University; Ramat Aviv; Israel |
Cancer | A-T Children's Project ; Wolfson Foundation ; European Union FP7 ; Israel Science Foundation |
PMID:21097778 PMID:18289391 |
biotools:spike, nlx_157705 | https://bio.tools/spike | SCR_010466 | Signaling Pathway Integrated Knowledge Engine | 2026-02-15 09:20:21 | 128 | ||||
|
NEBcutter Resource Report Resource Website 100+ mentions |
NEBcutter (RRID:SCR_010664) | service resource, analysis service resource, data analysis service, production service resource | 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. | bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: New England Biolabs |
PMID:12824395 | biotools:nebcutter, nlx_71778 | https://bio.tools/nebcutter | SCR_010664 | 2026-02-15 09:20:01 | 142 | ||||||||
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ComiR Resource Report Resource Website 10+ mentions |
ComiR (RRID:SCR_013023) | ComiR | service resource, analysis service resource, data analysis service, production service resource | 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. | mirna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Pittsburgh; Pennsylvania; USA |
NLM ; Fondazione RiMED |
PMID:23703208 PMID:23284279 |
Acknowledgement requested | OMICS_00395, biotools:comir | https://bio.tools/comir | SCR_013023 | Combinatorial miRNA targeting, ComiR: Combinatorial miRNA target prediction tool, ComiR - Combinatorial miRNA target prediction tool | 2026-02-15 09:20:41 | 26 | ||||
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omiRas Resource Report Resource Website 10+ mentions |
omiRas (RRID:SCR_010833) | omiRas | service resource, analysis service resource, data analysis service, production service resource | 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. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23946503 | biotools:omiras, OMICS_00383 | https://bio.tools/omiras | SCR_010833 | 2026-02-15 09:20:25 | 14 | |||||||
|
MutationTaster Resource Report Resource Website 1000+ mentions |
MutationTaster (RRID:SCR_010777) | MutationTaster | service resource, analysis service resource, data analysis service, production service resource | Evaluates disease-causing potential of sequence alterations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20676075 | Acknowledgement requested | biotools:mutation_taster, OMICS_00153 | https://bio.tools/mutation_taster | SCR_010777 | 2026-02-15 09:20:03 | 4180 | ||||||
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GenoREAD Resource Report Resource Website |
GenoREAD (RRID:SCR_012007) | GenoREAD | service resource, analysis service resource, data analysis service, production service resource | A sequence verification pipeline where users can submit trace files to verify if a clone''s physical sequence matches its reference sequence. | clone, verification, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Virginia Bioinformatics Institute |
PMID:23042248 | Acknowledgement requested | OMICS_01823, biotools:genoread | https://bio.tools/genoread | SCR_012007 | GenoREAD - Sequencing Verification Pipeline | 2026-02-15 09:20:28 | 0 | |||||
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PLAN2L Resource Report Resource Website |
PLAN2L (RRID:SCR_013346) | PLAN2L | data or information resource, database, service resource | 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. | text mining, bio-entity relation extraction, literature, information extraction, cell cycle, regulation, protein interaction, cellular location, flowering, leave, root, seed, gene, normalization, interaction, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Spanish National Cancer Research Center |
PMID:19520768 | OMICS_01192, biotools:plan2l | https://bio.tools/plan2l | SCR_013346 | PLAN2L: Plant Annotation to Literature, Plant annotation to literature | 2026-02-15 09:20:40 | 0 | ||||||
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DSAP Resource Report Resource Website 1+ mentions |
DSAP (RRID:SCR_013352) | DSAP | service resource, analysis service resource, data analysis service, production service resource | 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. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20478825 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:dsap, OMICS_00357 | https://bio.tools/dsap | SCR_013352 | 2026-02-15 09:20:43 | 8 | ||||||
|
HmtVar Resource Report Resource Website 10+ mentions |
HmtVar (RRID:SCR_017288) | data or information resource, database, service resource | 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. | manually, curated, data, variability, mitochondria, pathogenicity, mtDNA, variant, human, bio.tools |
uses: HmtDB - Human Mitochondrial DataBase uses: 1000 Genomes Project and AWS uses: MITOMAP - A human mitochondrial genome database uses: MutPred uses: SNPsandGO is listed by: Debian is listed by: bio.tools is affiliated with: University of Bologna; Bologna; Italy has parent organization: University of Bari; Bari; Italy |
Rosa Maria Massari fellowship from the Italian Association for Cancer Research ; DHOMOS Worldwide Cancer Research ; DISCO TRIP ; Italian Ministry of Health |
PMID:30371888 PMID:31821723 |
Free, Freely available | biotools:HmtVar | https://bio.tools/HmtVar | SCR_017288 | 2026-02-15 09:21:18 | 10 | ||||||
|
EGSEA Resource Report Resource Website 50+ mentions |
EGSEA (RRID:SCR_015036) | source code, software toolkit, software resource | 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. | gene set, rna sequencing, analysis method, r package, bio.tools |
is listed by: Debian is listed by: bio.tools is hosted by: Bioconductor |
Victorian State Government Operational Infrastructure Support ; Australian Government NHMRC IRIISS ; NHMRC GNT1050661; NHMRC GNT1045936; NHMRC GNT1057854; NHMRC GNT1104924 |
PMID:27694195 | Free, Available for download | biotools:egsea | https://bio.tools/egsea | SCR_015036 | Ensemble of Gene Set Enrichment Analyses (EGSEA), Ensemble of Gene Set Enrichment Analyses | 2026-02-15 09:21:05 | 62 | |||||
|
Embassy-domsearch Resource Report Resource Website |
Embassy-domsearch (RRID:SCR_016086) | source code, software toolkit, software resource | Source code for EMBOSS commands to search for protein domains. Its functions include removing redundant and fragment sequences from DHF files, generating PSI-BLAST hits (DHF file) from a DAF file, removing ambiguous classified sequences from DHF files, and generating DHF files from keyword search of UniProt. | dhf, daf, redundancy, protein, domain, psi-blast, uniprot, molecular, biology |
is used by: RAVEN is listed by: Debian |
Free, Available for download, Freely available | https://sources.debian.org/src/embassy-domsearch/ | SCR_016086 | 2026-02-15 09:21:31 | 0 | |||||||||
|
cwltool Resource Report Resource Website 10+ mentions |
cwltool (RRID:SCR_015528) | source code, software toolkit, software resource | Reference implementation of the Common Workflow Language standards. It provides complete features and tools and comprehensive validation of CWL. The reference implementation consists of two packages. The cwltool package is the primary Python module containing the reference implementation in the cwltool module and console executable by the same name. The cwlref-runner package is optional and provides an additional entry point under the alias cwl-runner, which is the implementation-agnostic name for the default CWL interpreter installed on a host. | language, reference implementation, python |
uses: Python Programming Language is listed by: Debian is listed by: OMICtools |
DOI:10.6084/m9.figshare.3115156.v2 | Available for download | OMICS_28977 | https://sources.debian.org/src/cwltool/ | SCR_015528 | CWLtool, Common Workflow Language Tool | 2026-02-15 09:20:55 | 24 | ||||||
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Bio-EUtilities Resource Report Resource Website |
Bio-EUtilities (RRID:SCR_024064) | software toolkit, software resource | Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic. | interacting, storing information, NCBI's eUtils interface, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-eutilities-perl/ | SCR_024064 | Bio-EUtilities - BioPerl low-level API for retrieving and storing data from NCBI eUtils, libbio-eutilities-perl | 2026-02-15 09:22:35 | 0 | ||||||||
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Bio-Tools-Run-Alignment-Clustalw Resource Report Resource Website |
Bio-Tools-Run-Alignment-Clustalw (RRID:SCR_024067) | software toolkit, software resource | Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program. | performing multiple sequence alignment, set of unaligned sequences, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-tools-run-alignment-clustalw-perl/ | SCR_024067 | libbio-tools-run-alignment-clustalw-perl, Bio-Tools-Run-Alignment-Clustalw - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program | 2026-02-15 09:23:32 | 0 | ||||||||
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Tab2MAGE Resource Report Resource Website |
Tab2MAGE (RRID:SCR_024101) | software library, software toolkit, software resource | Software package written and supported by the ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets.Tab2MAGE uses flexible spreadsheet format for MIAME annotation of microarray experiments.Spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange. | ArrayExpress, submitting large microarray experiment datasets, spreadsheet format for MIAME annotation of microarray experiments, | is listed by: Debian | Free, Available for download, Freely available, | https://tab2mage.sourceforge.net/ | https://sources.debian.org/src/mage2tab/ | SCR_024101 | mage2tab, ArrayExpress Tab2MAGE | 2026-02-15 09:23:22 | 0 | |||||||
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Bio-Tools-Phylo-PAML Resource Report Resource Website |
Bio-Tools-Phylo-PAML (RRID:SCR_024069) | software toolkit, software resource | Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output. | parse output, PAML programs, codeml, baseml, basemlg, codemlsites, yn00. | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-tools-phylo-paml-perl/ | SCR_024069 | libbio-tools-phylo-paml-perl, Bio-Tools-Phylo-PAML - Parses output from the PAML programs codeml, baseml, codemlsites and yn00, basemlg | 2026-02-15 09:23:22 | 0 | ||||||||
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Mapsembler2 Resource Report Resource Website 1+ mentions |
Mapsembler2 (RRID:SCR_024102) | software library, software toolkit, software resource | Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants. | Targeted assembly, NGS raw read, input sequences, | is listed by: Debian | PMID:22443449 | Free, Available for download, Freely available, | OMICS_18310 | https://sources.debian.org/src/mapsembler2/ | SCR_024102 | mapsembler2, Mapsembler | 2026-02-15 09:23:20 | 1 | ||||||
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MAXFLOW Resource Report Resource Website |
MAXFLOW (RRID:SCR_024103) | software library, software toolkit, software resource | Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph. | computing mincut/maxflow in a graph, | is listed by: Debian | DOI:10.1109/TPAMI.2004.60 | Free, Available for download, Freely available, | https://sources.debian.org/src/maxflow/ | SCR_024103 | maxflow | 2026-02-15 09:23:33 | 0 | |||||||
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Bio-Graphics Resource Report Resource Website |
Bio-Graphics (RRID:SCR_024061) | software toolkit, software resource | Software package to generate GD images of Bio::Seq objects. | generate GD images of Bio::Seq objects, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-graphics-perl/ | SCR_024061 | Bio-Graphics - Generate GD images of Bio-Seq objects, libbio-graphics-perl | 2026-02-15 09:23:21 | 0 |
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