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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Transporter Classification Database
 
Resource Report
Resource Website
100+ mentions
Transporter Classification Database (RRID:SCR_004490) TCDB, TC storage service resource, source code, software resource, service resource, production service resource, data analysis software, data repository, data analysis service, data or information resource, data processing software, software application, analysis service resource, database Curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from variety of living organisms based on IUBMB-approved transporter classification (TC) system. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. TC system is analogous to Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information. TCDB users may submit their own sequenced proteins and descriptions for inclusion into database. The software tools used are all freely available for download. These programs are used for analysis of Protein and DNA sequences. Programs require UNIX server to run. membrane transport, protein sequence, transporter, bio.tools, FASEB list is recommended by: National Library of Medicine
is listed by: bio.tools
is listed by: Debian
has parent organization: University of California at San Diego; California; USA
NIGMS GM1077402 PMID:19022853
PMID:16381841
Free, Freely available nlx_47724, biotools:tcdb https://bio.tools/tcdb SCR_004490 Transporter Classification Database 2026-08-06 09:26:09 311
SMART
 
Resource Report
Resource Website
5000+ mentions
SMART (RRID:SCR_005026) SMART software resource, service resource, data access protocol, production service resource, data analysis service, data or information resource, web service, analysis service resource, database Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures. extracellular, gene, genetic, genetically, genome, architecture, chromatin, domain, mobile, phyletic, protein, proteome, signaling, structure, taxonomic, tertiary, bio.tools, FASEB list is used by: Mutation Annotation and Genomic Interpretation
is listed by: bio.tools
is listed by: Debian
is related to: Eukaryotic Linear Motif
is related to: Conserved Domain Database
is related to: GOTaxExplorer
has parent organization: EMBL - Bork Group
European Union PMID:18978020
PMID:16381859
PMID:14681379
PMID:10592234
PMID:9847187
PMID:9600884
Free, Freely available nif-0000-03471, biotools:smart http://smart.embl-heidelberg.de/, https://bio.tools/smart SCR_005026 Simple Modular Architecture Research Tool 2026-08-06 09:26:19 6760
NCBI BLAST
 
Resource Report
Resource Website
10000+ mentions
NCBI BLAST (RRID:SCR_004870) BLAST sequence analysis software, software resource, data access protocol, data analysis software, web service, data processing software, software application Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences. genome, similarity, sequence, nucleotide, protein, gene, data, bio.tools is used by: MITE-Tracker
is used by: Cello2Go
is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: G-BLASTN
is related to: genBlastA
has parent organization: NCBI
is required by: RelocaTE
works with: Whole Genome Shotgun (WGS) Project
works with: BLASTClust
works with: MOLE-BLAST
works with: Genotyping
National Library of Medicine PMID:16845079
PMID:18440982
Free, Freely available, Tutorial available OMICS_01436, nlx_84530, biotools:blast http://blast.ncbi.nlm.nih.gov, https://bio.tools/blast, https://sources.debian.org/src/ncbi-blast+/ SCR_004870 NCBI Basic Local Alignment Search Tool, NCBI BLAST, Basic Local Alignment Search Tool, BLAST 2026-08-06 09:26:15 15381
ngsTools
 
Resource Report
Resource Website
50+ mentions
ngsTools (RRID:SCR_005489) ngsTools data analysis software, software application, software resource, data processing software A collection of software programs for population genetics analyses from NGS (Next-Generation Sequencing) data, taking into account its statistical uncertainty. The methods implemented in these programs do not rely on SNP (Single Nucleotide Polymorphism) or genotype calling, and are particularly suitable for low sequencing depth data. java, next-generation sequencing, population, genetics, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
PMID:24458950 GNU General Public License, v3, Acknowledgement requested OMICS_02248, biotools:ngstools https://bio.tools/ngstools SCR_005489 2026-08-06 09:26:25 53
SolexaQA
 
Resource Report
Resource Website
100+ mentions
SolexaQA (RRID:SCR_005421) SolexaQA sequence analysis software, software resource, data analysis software, data processing software, data visualization software, software application Software package to calculate sequence quality statistics and create visual representations of data quality for Illumina's second-generation sequencing technology. bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: SourceForge
PMID:20875133 Acknowledgement requested biotools:solexaqa, OMICS_01078 https://bio.tools/solexaqa SCR_005421 2026-08-06 09:26:24 291
PHAge Search Tool
 
Resource Report
Resource Website
100+ mentions
PHAge Search Tool (RRID:SCR_005184) PHAST data set, service resource, production service resource, data analysis service, data or information resource, analysis service resource A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage cornerstone feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage quality and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. Databases available for download include Virus DB, Prophage and virus DB, Bacteria DB, and PHAST result DB. Pre-calculated genomes for viewing are also available. prophage sequence, genome, prophage, sequence, bacterial genome, plasmid, dna sequence, graph, phage, annotate, virus, nucleotide sequence, fasta, annotated genome, genbank, bio.tools, FASEB list is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: University of Alberta; Alberta; Canada
PMID:21672955 Acknowledgement requested biotools:phast, OMICS_00180 https://bio.tools/phast SCR_005184 PHAST - PHAge Search Tool 2026-08-06 09:26:22 225
FLASH
 
Resource Report
Resource Website
1000+ mentions
FLASH (RRID:SCR_005531) FLASh sequence analysis software, software resource, data analysis software, data processing software, software application Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data. bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: shovill
is related to: CLIP-Explorer
has parent organization: Johns Hopkins University; Maryland; USA
NLM R01 LM006845;
NIGMS R01 GM083873;
NHGRI R01 HG006677
PMID:21903629 Free, Available for download, Freely available biotools:flash, OMICS_01047 https://sourceforge.net/projects/flashpage/files/, https://bio.tools/flash, https://sources.debian.org/src/flash/ SCR_005531 Fast Length Adjustment of SHort reads, Fast Length Adjustment of Short reads 2026-08-06 09:26:27 2175
CLIPZ
 
Resource Report
Resource Website
10+ mentions
CLIPZ (RRID:SCR_005755) CLIPZ service resource, production service resource, data analysis service, data or information resource, analysis service resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets. rna-binding protein, binding site, protein, functional annotation, cross-linking and immunoprecipitation, short read, mrna-seq, digital gene expression, small rna cloning, visualization, mining, analysis, post-transcriptional regulatory element, genome, transcript, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: SIB Swiss Institute of Bioinformatics
has parent organization: University of Basel; Basel; Switzerland
PMID:21087992 THIS RESOURCE IS NO LONGER IN SERVICE. OMICS_02256, biotools:clipz https://bio.tools/clipz SCR_005755 2026-08-06 09:26:29 20
Sybil
 
Resource Report
Resource Website
10+ mentions
Sybil (RRID:SCR_005593) Sybil database, data or information resource, software resource A web-based software package for comparative genomics. comparative genomics, genome, synteny, protein cluster, protein, gene, genomic region, synteny gradient, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: SourceForge
PMID:22121156 OMICS_00945, biotools:sybil https://bio.tools/sybil SCR_005593 Sybil: Web-based software for comparative genomics 2026-08-06 09:26:27 37
959 Nematode Genomes
 
Resource Report
Resource Website
1+ mentions
959 Nematode Genomes (RRID:SCR_006068) NematodeGenomes wiki, narrative resource, data or information resource A collaborative wiki that collates information on completed, ongoing and planned genome and transcriptome sequencing projects on species from phylum Nematoda. The intention is to encourage genome sequencing across the diversity of the phylum Nematoda. Wiki includes: * Published complete nematode genomes: A dynamically generated table of all species for which the genome is published. * Nematode species with genomes in progress: A dynamically generated table of all species for which a genome project is underway. Users may add species to the list * Proposed nematode genome projects: To propose a species for genome sequencing, edit its species page, and set the genome project status to proposed. * BLAST server: Search a number of the nematode-genomes-in-progress with genes of your choice. Currently there are 12 draft genomes available... * Genomes with Data available: Genomes with data available for download. Users may add more data URLs to strain pages or update the URLs. nematode, genome, genome sequencing, transcriptome sequencing, blast, genomics, sequencing, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: nematodes.org
has parent organization: University of Edinburgh; Scotland; United Kingdom
NERC PMID:22058131 nlx_151473, biotools:959_nematode_genomes https://bio.tools/959_nematode_genomes SCR_006068 NematodeGenomes 2026-08-06 09:26:29 2
MMMDB - Mouse Multiple tissue Metabolome DataBase
 
Resource Report
Resource Website
1+ mentions
MMMDB - Mouse Multiple tissue Metabolome DataBase (RRID:SCR_006064) MMMDB service resource, production service resource, data analysis service, data or information resource, analysis service resource, database MMMDB, Mouse Multiple tissue Metabolome DataBase, is a freely available metabolomic database containing a collection of metabolites measured from multiple tissues from single mice. The datases are collected using a single instrument and not integrated from literatures, which is useful for capturing the holistic overview of large metabolomic pathway. Currently data from cerabra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, and plasma are provided. Non-targeted analyses were performed by capillary electropherograms time-of-flight mass spectrometry (CE-TOFMS) and, therefore, both identified metabolites and unknown (without matched standard) peaks were uploaded to this database. Not only quantified concentration but also processed raw data such as electropherogram, mass spectrometry, and annotation (such as isotope and fragment) are provided. metabolite, metabolome, cerabra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, plasma, metabolomic pathway, capillary electropherograms time-of-flight mass spectrometry, electropherogram, mass spectrometry, annotation, isotope, fragment, bio.tools is listed by: Debian
is listed by: bio.tools
PMID:22139941 Free nlx_151467, biotools:mmmdb https://bio.tools/mmmdb SCR_006064 Mouse Multiple tissue Metabolome DataBase 2026-08-06 09:26:29 1
InterEvol database
 
Resource Report
Resource Website
10+ mentions
InterEvol database (RRID:SCR_006054) InterEvol software resource, service resource, production service resource, data analysis service, data or information resource, analysis service resource, database InterEvol database is designed for the analysis of co-evolution events at the interface of known structures of hetero- and homo-oligomers. The database can be search and analyzed through 3 interconnected levels of analysis: * From a Keyword or the PDB entry of a complex, you can browse: ** structural homologs for every chain in other complexes ** structural interologs for every interface ** retrieve pre-computed sequence alignments in diverse species * From 1 or 2 sequences of interacting partners: ** build 2 multiple sequence alignments with the same species ordered in each ** query the InterEvol database with alignments using profile-profile comparison method * Visualize structure vs sequence alignment at the complex interface ** A dedicated Pymol plugin is provided ** Alignment views in Pymol are interactively restricted to the residues selected at the interface structure, evolution, protein complex, interface, protein complex, sequence alignment, plug in, protein structure, visualization, pymol plugin, structural homolog, structural interolog, bio.tools is listed by: Debian
is listed by: bio.tools
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
has parent organization: CEA; Gif sur Yvette; France
Commissariat a lEnergie Atomique ;
ANR HPGenVar
PMID:22053089 Free and open to all users - no login requirement nlx_151453, biotools:interevol https://bio.tools/interevol SCR_006054 2026-08-06 09:26:32 10
ICEberg
 
Resource Report
Resource Website
50+ mentions
ICEberg (RRID:SCR_006026) ICEberg service resource, production service resource, data analysis service, data or information resource, analysis service resource, database ICEberg is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. ICEberg will facilitate efficient, multidisciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community. dna, protein, sequence, chromosome, element, gene, similarity search, sequence alignment, genome, phylogenetic, functional analysis, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
has parent organization: Shanghai Jiao Tong University; Shanghai; China
National Natural Science Foundation of China 973 program 2009CB118901;
National Natural Science Foundation of China 973 program 2012CB721002;
National Natural Science Foundation of China 863 program 2011BAD23B05-3;
Ministry of Science and Technology China ;
Ministry of Education China NCET-10-0572;
Shanghai Jiaotong University ;
Shanghai Municipality ;
Action Medical Research SP4255;
Innovation Fellowship ;
East Midlands Development Agency
PMID:22009673 nlx_151424, biotools:iceberg https://bio.tools/iceberg SCR_006026 ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria 2026-08-06 09:26:30 77
Europe PubMed Central
 
Resource Report
Resource Website
500+ mentions
Europe PubMed Central (RRID:SCR_005901) Europe PMC, UKPMC software resource, data access protocol, web service, data or information resource, bibliography, database Free access to biomedical literature resources including all of PubMed and PubMed Central, agricultural abstracts (from AGRICOLA), over 4 million international life science patents abstracts, National Health Service (NHS) clinical guidelines, and is supplemented with Chinese Biological Abstracts and the Citeseer database. As well as powerful search of abstracts and full text articles, it also includes: * article citations and sort order based on citation count * data citations mined from full text articles * links to and from related databases and institutional repositories * a tool to create bibliographies linked to your ORCID * named entity recognition of keywords and text-mining-based applications showcased in Europe PMC Labs * Tools for recipients of grants from one of the Europe PMC funders to deposit full-text manuscripts and link them to those specific grants. * Web services for programmatic access to all the above bibliographic information and 50,000 grants. * Search by publication date, relevance, or the number of times an article has been cited. * Links to public databases such as UniProt, Protein Data Bank (PDBe), and the European Nucleotide Archive (ENA) are provided. * Through textmining technologies, you can highlight and browse keywords such as gene names, organisms and diseases. * Search 40,000 biomedical research grants awarded to the 18,000 PIs supported by the Europe PMC funders. * Roadtest new tools based on Europe PMC content in Europe PMC labs. * In Europe PMC plus, PIs supported by the Europe PMC funders can link grants to publication information, view article citation and download statistics, and submit manuscripts. biomedical, literature, publication, health, life science, patent, clinical guideline, grant, text mining, author identification, archiving, open access, gold standard, bio.tools, bio.tools, FASEB list uses: EvidenceFinder
uses: BioLexicon
is listed by: FORCE11
is listed by: Debian
is listed by: bio.tools
is related to: PubMed
is related to: PubMed Central
is related to: AGRICOLA
is related to: ORCID - Open Researcher and Contributor ID
is related to: EvidenceFinder
has parent organization: European Bioinformatics Institute
has parent organization: Mimas
has parent organization: National Centre for Text Mining
is parent organization of: EvidenceFinder
Wellcome Trust WT098231 PMID:21062818 Free, The community can contribute to this resource nlx_149472, biotools:europe_pmc, biotools:ukpmc https://bio.tools/ukpmc, https://bio.tools/europe_pmc http://ukpmc.ac.uk/ SCR_005901 UK PubMed Central 2026-08-06 09:26:28 505
pickgene
 
Resource Report
Resource Website
pickgene (RRID:SCR_001331) pickgene data analysis software, software application, software resource, data processing software Software for adaptive Gene Picking for Microarray Expression Data Analysis. microarray, gene expression, differential expression, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Bioconductor
Free, Available for download, Freely available OMICS_02007, biotools:pickgene https://bio.tools/pickgene SCR_001331 2026-08-06 09:25:22 0
VCFtools
 
Resource Report
Resource Website
1000+ mentions
VCFtools (RRID:SCR_001235) data management software, software application, software resource Software package for working with VCF files. Used to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.Implements various utilities for processing Variant Call Format files, including validation, merging, comparing. Provides general Perl API. perl, genetic variation, variant call format, software, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
PMID:21653522
DOI:10.1093/bioinformatics/btr330
Free, Available for download, Freely available OMICS_02105, biotools:vcftools, SCR_012092, OMICS_05112 https://bio.tools/vcftools, https://sources.debian.org/src/vcftools/ http://vcftools.sourceforge.net/ SCR_001235 Variant Call Format Tools 2026-08-06 09:25:21 4095
ShortFuse
 
Resource Report
Resource Website
1+ mentions
ShortFuse (RRID:SCR_001107) sequence analysis software, software resource, data analysis software, data processing software, software application THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A software package with tools for identifying fusion transcripts from RNA-Seq data. It is written in C++, and has dependencies on packages from Python 2. fusion transcripts, rna, sequence data, python 2, c++, sequence analysis software, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
PMID:21330288 THIS RESOURCE IS NO LONGER IN SERVICE biotools:shortfuse, OMICS_01355 https://bio.tools/shortfuse SCR_001107 2026-08-06 09:25:19 1
metahdep
 
Resource Report
Resource Website
metahdep (RRID:SCR_001225) metahdep data analysis software, software application, software resource, data processing software THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies. differential expression, microarray, gene expression, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Bioconductor
PMID:19648140 THIS RESOURCE IS NO LONGER IN SERVICE biotools:metahdep, OMICS_02121 https://bio.tools/metahdep SCR_001225 metahdep - Hierarchical Dependence in Meta-Analysis 2026-08-06 09:25:21 0
globaltest
 
Resource Report
Resource Website
10+ mentions
globaltest (RRID:SCR_001256) globaltest sequence analysis software, software resource, data analysis software, data processing software, software application A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms. differential expression, go, microarray, one channel, pathway, bio.tools uses: KEGG
is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: Gene Ontology
has parent organization: Bioconductor
PMID:34046931 Free, Available for download, Freely available biotools:globaltest, OMICS_02084 https://bio.tools/globaltest SCR_001256 2026-08-06 09:25:21 30
DSRC
 
Resource Report
Resource Website
1+ mentions
DSRC (RRID:SCR_001005) DSRC data management software, software application, software resource An application designed for compression of data files containing reads from DNA sequencing in FASTQ format. Its main features include multithreaded compression of FASTQ output, python and C++ libraries, and support for lossy IDs compression. fastq, dna sequence, compression, multithread, data management software, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
PMID:21252073 Free, Available as binary, Available as source code biotools:dsrc, OMICS_00955 https://bio.tools/dsrc SCR_001005 DNA Sequence Reads Compression, DNA Sequence Reads Compression (DSRC) 2026-08-06 09:25:18 1

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