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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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VBASE2 Resource Report Resource Website 50+ mentions |
VBASE2 (RRID:SCR_007082) | VBASE2 | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse. It presents V gene sequences extracted from the EMBL nucleotide sequence database and Ensembl together with links to the respective source sequences. Based on the properties of the source sequences, V genes are classified into 3 different classes: * Class 1: genomic and rearranged evidence * Class 2: genomic evidence only * Class 3: rearranged evidence only This allows careful sequence quality validation by the user. References to other immunological databases ( KABAT, IMGT/LIGM and VBASE ) are given to provide all public annotation data for each V gene. The VBASE2 database can be accessed either by the Direct Query interface or by the DNAPLOT Query interface. The Sequences given by the user are aligned with DNAPLOT against the VBASE2 database. Direct Query allows to enter sequence IDs and names (Field 1), choose species, locus, V gene family and class (Field 2) or search for 100% sequences (Field 3). At the DNAPLOT Query, the sequences given by the user are aligned with DNAPLOT against the VBASE2 database. The DNAPLOT program offers V gene nucleotide sequence alignment referring to the IMGT V gene unique numbering. The Quick Search can be used either for Direct Query to search for sequence IDs and V gene names or for DNAPLOT Query for up to 5 sequences. The new Fab Analysis allows you to align Fab, scFab, scAb or scFv sequences with DNAPLOT against the VBASE2 database, where both heavy and light chain are analyzed. | v gene sequence, v gene, gene, dna, sequence, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: European Nucleotide Archive (ENA) is related to: Ensembl |
BMBF 031U110A/031U210A | PMID:15608286 | Acknowledgement requested | nlx_25238, biotools:germ-line_v_genes | https://bio.tools/germ-line_v_genes | SCR_007082 | VBASE2: the integrative germ-line V gene database | 2026-07-28 09:41:50 | 72 | ||||
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BioEdit Resource Report Resource Website 10000+ mentions |
BioEdit (RRID:SCR_007361) | software application, data analysis software, sequence analysis software, software resource, data processing software, alignment software, image analysis software | Software tool as biological sequence alignment editor written for Windows 95/98/NT/2000/XP/7 and sequence analysis program. Provides sequence manipulation and analysis options and links to external analysis programs to view and manipulate sequences with simple point and click operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence, alignment, editor, analysis, program | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156845 | SCR_007361 | 2026-07-28 09:41:58 | 13339 | |||||||||
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Olfactory Receptor DataBase Resource Report Resource Website 1+ mentions |
Olfactory Receptor DataBase (RRID:SCR_007830) | ORDB | service resource, data or information resource, data repository, data analysis service, storage service resource, database, production service resource, analysis service resource | Database of vertebrate olfactory receptors genes and proteins. It supports sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family. The database also incorporates a broad range of chemosensory genes and proteins, including the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfaction receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), and fungal pheromone receptors (FPRs). ORDB currently houses chemosensory receptors for more than 50 organisms. ORDB contains public and private sections which provide tools for investigators to analyze the functions of these very large gene families of G protein-coupled receptors. It also provides links to a local cluster of databases of related information in SenseLab, and to other relevant databases worldwide. The database aims to house all of the known olfactory receptor and chemoreceptor sequences in both nucleotide and amino acid form and serves four main purposes: * It is a repository of olfactory receptor sequences. * It provides tools for sequence analysis. * It supports similarity searches (screens) which reduces duplicate work. * It provides links to other types of receptor information, e.g. 3D models. The database is accessible to two classes of users: * General public www users have full access to all the public sequences, models and resources in the database. * Source laboratories are the laboratories that clone olfactory receptors and submit sequences in the private or public database. They can search any sequence they deposited to the database against any private or public sequence in the database. This user level is suited for laboratories that are actively cloning olfactory receptors. | fungal, pheromone receptor, gene, chemosensory, chemosensory receptor, g protein-coupled receptor, olfaction receptor, protein, receptor, taste papilla receptor, vomeronasal organ receptor, olfactory receptor, nucleotide, amino acid, chemoreceptor sequence, olfactory receptor sequence, chemoreceptor, sequence |
is used by: NIF Data Federation is listed by: 3DVC is related to: Odor Molecules DataBase is related to: Integrated Manually Extracted Annotation has parent organization: Yale School of Medicine; Connecticut; USA |
Aging | Human Brain Project ; NIMH ; NIA ; NICD ; NINDS ; Multidisciplinary University Research Initiative ; National Aeronautics and Space Administration ; NIDCD RO1 DC 009977; NIDCD P01 DC 04732; NLM G08 LM05583 |
PMID:11752336 PMID:9847223 PMID:9218144 |
Public, Private, Acknowledgement requested, The community can contribute to this resource | nif-0000-03213 | SCR_007830 | Olfactory Receptors Database | 2026-07-28 09:41:54 | 4 | ||||
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Gene3D Resource Report Resource Website 100+ mentions |
Gene3D (RRID:SCR_007672) | Gene3D | service resource, data or information resource, data repository, database, data access protocol, software resource, web service, storage service resource | A large database of CATH protein domain assignments for ENSEMBL genomes and Uniprot sequences. Gene3D is a resource of form studying proteins and the component domains. Gene3D takes CATH domains from Protein Databank (PDB) structures and assigns them to the millions of protein sequences with no PDB structures using Hidden Markov models. Assigning a CATH superfamily to a region of a protein sequence gives information on the gross 3D structure of that region of the protein. CATH superfamilies have a limited set of functions and so the domain assignment provides some functional insights. Furthermore most proteins have several different domains in a specific order, so looking for proteins with a similar domain organization provides further functional insights. Strict confidence cut-offs are used to ensure the reliability of the domain assignments. Gene3D imports functional information from sources such as UNIPROT, and KEGG. They also import experimental datasets on request to help researchers integrate there data with the corpus of the literature. The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes. Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins. The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | protein domain, protein, protein superfamily, hidden markov model, structural domain, genome, sequence, domain assignments, protein structure, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University College London; London; United Kingdom |
NIH ; Wellcome Trust ; European Union FP6 ENFIN LSHG-CT-2003-503265; European Union FP6 ENFIN LSHG-CT-2004-512092; European Union FP6 ENFIN LSHG-CT-2005-518254; DOE DE-AC02-065CH11357 |
PMID:19906693 PMID:18032434 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02877, biotools:gene3d | https://bio.tools/gene3d | SCR_007672 | Gene3D - Structures assigned to Genomes | 2026-07-28 09:42:09 | 272 | ||||
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Organelle DB Resource Report Resource Website 1+ mentions |
Organelle DB (RRID:SCR_007837) | Organelle DB | service resource, data or information resource, data repository, database, image collection, d spatial image, storage service resource | Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization. Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light. | gene, fly, vertebrate, human, mouse, plant, worm, yeast, protein, k-12, organelle, protein localization, function, subcellular structure, protein complex, sequence, annotation, micrograph, visualization, data analysis service |
is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
American Cancer Society Research Scholar Grant RSG-06-179-01-MBC; March of Dimes Basil O'Connor Starter Scholar Research award 5-FY05-1224; NSF DBI-0543017 |
PMID:17130152 PMID:15608270 |
Free, Acknowledgement requested | nif-0000-03226 | SCR_007837 | Organelle DB: A Database of Organelles and Protein Complexes | 2026-07-28 09:41:54 | 7 | |||||
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Protein Mutant Database Resource Report Resource Website 1+ mentions |
Protein Mutant Database (RRID:SCR_007878) | PMD | service resource, data or information resource, data repository, database, storage service resource | It provides information on natural and artificial mutants, including random and site-directed ones, for all proteins except members of the globin and immunoglobulin families. The PMD is based on literature, and each entry in the database corresponds to one article which may describe one, several or a number of protein mutants. Each database entry is identified by a serial number and is defined as either natural or artificial, depending on the type of the mutation. For each entry the following are recorded : JOURNAL, TITLE, CROSS-REFERENCE, PROTEIN, N-TERMINAL, CHANGE, FUNCTION, STRUCTURE, STABILITY, etc. CROSS-REFERENCE indicates the code names of the protein given in other databases such as Protein Identification Resources (2). N-TERMINAL shows the N-terminal sequence of five amino acids which may help to show the unambiguous numbering of th e sequence. CHANGE indicates the position and kind of mutations, such as amino acid substitution, insertion and deletion, denoted with a specific notation. Any functional or structural features (FUNCTION, STRUCTURE, STABILITY,etc) observed in the mutant are described immediately after ''CHANGE''. Relative differences in activity and/or stability, in comparison with the wild-type protein, are indicated with symbols (- -),(-),(=),(+) or (+ +). Complete loss of activity is denoted as (0). Data Submission A data submission system was newly prepared in the PMD. We welcome the authors of articles published in academic journals to submit their own mutant data to the PMD. After checking the contents, we will register the data with a unique accession number. | amino acid, artificial, deletion, insertion, mutant, natural, protein, sequence, substitution |
is related to: PredictSNP has parent organization: National Institute of Genetics; Shizuoka; Japan |
SCR_007878 | Protein Mutant Database | 2026-07-28 09:42:14 | 4 | |||||||||
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REBASE Resource Report Resource Website 100+ mentions |
REBASE (RRID:SCR_007886) | REBASE | data or information resource, database | Database of information about restriction enzymes and related proteins containing published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Several tools are available including REBsites, BLAST against REBASE, NEBcutter and REBpredictor. Putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. REBASE is updated daily and is constantly expanding. Users may submit new enzyme and/or sequence information, recommend references, or send them corrections to existing data. The contents of REBASE may be browsed from the web and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email., | endonuclease, enzyme, genome, archaeal, bacterial, cleavage, crystal, dna, individual protein family databases, isochizomer, methylation, methyltransferase, modification, protein, recognition, restriction, restriction enzyme, sensitivity, sequence, site, methylase, cleavage site, restriction-modification, blast, FASEB list |
has parent organization: New England Biolabs works with: Webcutter |
New England Biolabs Inc ; NLM LM04971 |
PMID:19846593 PMID:17202163 |
r3d100012171, nif-0000-03391 | http://rebase.neb.com, https://doi.org/10.17616/R3J930 | http://www.neb.com/rebase | SCR_007886 | The Restriction Enzyme Database, Restriction Enzyme Database | 2026-07-28 09:41:55 | 246 | ||||
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MAxEntScan Resource Report Resource Website 50+ mentions |
MAxEntScan (RRID:SCR_016707) | MAxEntScan | software application, service resource, simulation software, software resource | Software tool as a framework for modeling the sequences of short sequence motifs based on the maximum entropy principle (MEP). Used for sequence motifs such as those involved in RNA splicing. | modeling, sequence, short, motif, maximum, entropy, principle, MEP, RNA, splicing |
is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
NSF Grant 0218506; NIH ; Lee Kuan Yew Scholarship for the goverment of Singapore |
PMID:15285897 | Free, Available for download, Freely available | SCR_016707 | Maximum Entropy Scan, MAxEntScan, MAximumEntropyScan | 2026-07-28 09:44:21 | 65 | ||||||
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Discovar assembler Resource Report Resource Website 10+ mentions |
Discovar assembler (RRID:SCR_016755) | Discovar | software application, data analysis software, sequence analysis software, software resource, data processing software | Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes. | variant, calling, reference, de novo, assembly, genome, genetic, human, sequence, analysis |
is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG003474; NHGRI U54 HG003067; NIAID HHSN272200900018C |
PMID:25326702 | Free, Available for download, Freely available | SCR_016755 | Discovar de novo, Discovar | 2026-07-28 09:44:26 | 20 | ||||||
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rsfMRI_fconn calculation Resource Report Resource Website 1+ mentions |
rsfMRI_fconn calculation (RRID:SCR_016591) | rsfMRI_fconn calculation | software application, software resource, data analysis software, data processing software | Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity. | data, resting, state, brain, processing, functional, magnetic, resonance, imaging, measurement, calculate, region, connectivity, analysis, sequence |
uses: SPM is related to: MATLAB |
SCR_016591 | resting state functional MRI and functional connectivity calculation, resting state functional MRI pre processing and Functional Connectivity calculation | 2026-07-28 09:44:21 | 1 | |||||||||
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Entrez Resource Report Resource Website 10+ mentions |
Entrez (RRID:SCR_016640) | data or information resource, data access protocol, software resource, web service, portal | Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ. | global, query, cross, database, search, retrival, system, database, nucleotide, protein, sequence, data, genomic, mapping, structure, reference |
is affiliated with: PubChem BioAssay is related to: National Library of Medicine has parent organization: NCBI works with: Batch Entrez works with: Biotite |
Free, Freely available | SCR_016640 | 2026-07-28 09:44:20 | 15 | ||||||||||
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MOLE-BLAST Resource Report Resource Website 1+ mentions |
MOLE-BLAST (RRID:SCR_016644) | moleblast, Mole Blast, MOLE BLAST | software application, data analysis software, sequence analysis software, data access protocol, software resource, data processing software, web service | Software tool that helps taxonomists find closest database neighbors of submitted query sequences by generating a phylogenetic tree from BLAST results. | taxonomist, find, close, database, submitted, query, sequence, generate, phylogenetic, tree, nucleotide | works with: NCBI BLAST | Free, Freely available | SCR_016644 | 2026-07-28 09:44:23 | 1 | |||||||||
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Clonotator Resource Report Resource Website |
Clonotator (RRID:SCR_016730) | software application, data analysis software, sequence analysis software, data access protocol, software resource, data processing software, alignment software, web service, image analysis software | Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data. | screening, annotation, cDNA, sequence, amino acid, align, reference, database, protein, disease, mutation, transcriptomic, data | has parent organization: University of California at San Francisco; California; USA | Free, Freely available, Registration required | https://willseylab.com/clonotator/ | SCR_016730 | 2026-07-28 09:44:24 | 0 | |||||||||
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VecScreen Resource Report Resource Website 10+ mentions |
VecScreen (RRID:SCR_016577) | software application, service resource, data analysis software, sequence analysis software, software resource, data processing software | Software tool to screen a nucleic acid sequence for vector contamination. Detects foreign DNAs such as vector, linker, adapter, and primer regions involved in nucleotide sequences by using blast search against vector sequence database. The main unit of this tool is vecscreen program obtainable from NCBI. | screen, sequence, nucleic acid, segment, vector, contamination | is listed by: OMICtools | Free, Available for download, Freely available | https://www.ddbj.nig.ac.jp/vecscreen-help-e.html | SCR_016577 | 2026-07-28 09:44:18 | 48 | |||||||||
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Rsubread Resource Report Resource Website 100+ mentions |
Rsubread (RRID:SCR_016945) | software application, data analysis software, software resource, data processing software, alignment software, image analysis software | Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers. | sequence, alignment, counting, multi, seed, strategy, mapping, read, reference, genome, analysis, data, SNP, calling, mutation, discovery, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: Subread |
Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support ; Australian Government |
PMID:23558742 | Free, Available for download, Freely available | biotools:rsubread | https://bio.tools/rsubread | SCR_016945 | 2026-07-28 09:44:25 | 188 | ||||||
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Biostrings Resource Report Resource Website 100+ mentions |
Biostrings (RRID:SCR_016949) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. | manipulation, biological, string, memory, efficient, container, sequence, set, DNA, RNA, protein |
is used by: riboWaltz is listed by: Bioconductor is related to: R Project for Statistical Computing has parent organization: Stanford University; Stanford; California |
Free, Available for download, Freely available | https://web.stanford.edu/class/bios221/labs/biostrings/lab_1_biostrings.html | SCR_016949 | 2026-07-28 09:44:25 | 167 | |||||||||
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ProSight Lite Resource Report Resource Website 10+ mentions |
ProSight Lite (RRID:SCR_016908) | software application, software resource, data analysis software, data processing software | Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data. | matching, single, protein, sequence, proteomics, top-down proteomics, mass, spectrometric, data, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Northwestern University; Illinois; USA is provided by: National Resource for Translational and Developmental Proteomics |
NIGMS R01 GM067193; NIDA P30 DA018310 |
DOI:10.1002/pmic.201400313 | Free, Available for download, Freely available | biotools:prosigh_lite | https://bio.tools/prosight_lite | SCR_016908 | 2026-07-28 09:44:26 | 14 | ||||||
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rnaSPAdes Resource Report Resource Website 50+ mentions |
rnaSPAdes (RRID:SCR_016992) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9. | assembling, transcript, RNA-Seq, data, single, cell, genome, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: SPAdes is related to: rnaQUAST |
Russian Science Foundation 14-50-00069 | DOI:10.1101/420208 | Free, Available for download, Freely available | biotools:rnaSPAdes_autogenerated | https://bio.tools/rnaSPAdes_autogenerated | SCR_016992 | 2026-07-28 09:44:26 | 53 | ||||||
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PPR-Meta Resource Report Resource Website 1+ mentions |
PPR-Meta (RRID:SCR_016915) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software tool to identify metagenomic sequences of phages, chromosomes or plasmids. Used for identifying phages and plasmids from metagenomic fragments using deep learning., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | identify, metagenomic, sequence, phage, chromosome, plasmid, fragment, machine, learning |
is related to: Python Programming Language is related to: MATLAB is related to: tensorflow |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/zhenchengfang/PPR-Meta | SCR_016915 | 2026-07-28 09:44:26 | 4 | |||||||||
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Nuclear Hormone Receptor Scan Resource Report Resource Website 1+ mentions |
Nuclear Hormone Receptor Scan (RRID:SCR_016975) | NHR-scan | service resource, data access protocol, software resource, production service resource, web service, analysis service resource | Web interface for computational prediction of nuclear hormone receptor binding sites in genomic sequences. Flexible Hidden Markov Model framework to allow for variable spacing and orientation of half sites. Allows for parameter modifications. | prediction, nuclear, hormone, receptor, binding, site, genomic, sequence, parameter, modification, analysis | is listed by: OMICtools | Pharmacia Corporation to the Center for Genomics and Bioinformatics ; Canadian Institutes of Health Research |
PMID:15563547 | Free, Available, Acknowledgement requested | OMICS_14042 | SCR_016975 | NHR-scan, NHR Scan, NHRScan, Nuclear Hormoe Receptor Scan | 2026-07-28 09:44:25 | 5 |
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