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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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T3DB Resource Report Resource Website 10+ mentions |
T3DB (RRID:SCR_002672) | T3DB | database, data or information resource | Database that combines detailed toxin data with comprehensive toxin target information. The database currently houses 3,053 toxins described by 32,276 synonyms, including pollutants, pesticides, drugs, and food toxins, which are linked to 1,670 corresponding toxin target records. Altogether there are 37,084 toxin, toxin target associations. (March 2014) Each toxin record (ToxCard) contains over 50 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information. This information has been extracted from over 5,454 sources sources, which include other databases, government documents, books, and scientific literature. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases. It is also fully searchable and supports extensive text, sequence, chemical structure, and relational query searches | toxicology, toxin, pollutant, pesticide, drug, food, gene-drug, interaction, gene, phenotype, mechanism, bio.tools |
is used by: NIF Data Federation is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: FMA has parent organization: University of Alberta; Alberta; Canada |
Alberta Advanced Education and Technology ; Canadian Institutes of Health Research ; Genome Alberta ; Genome Canada |
PMID:19897546 | Free, Available for download, Freely available | r3d100012189, nif-0000-22933, biotools:t3db, OMICS_01592 | https://bio.tools/t3db, https://doi.org/10.17616/R3VM0R | SCR_002672 | Toxin-Target Database, Toxin Toxin-Target Database, Toxin and Toxin Target Database, Toxin, Toxin Toxin Target Database | 2026-08-06 09:25:41 | 24 | ||||
|
HINT Resource Report Resource Website 100+ mentions |
HINT (RRID:SCR_002762) | HINT | database, data or information resource | A database of high-quality protein-protein interactions in different organisms. | protein-protein interaction, bio.tools, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Cornell University; New York; USA |
PMID:22846459 | Free, Freely available, Available for download | OMICS_02898, biotools:hint | https://bio.tools/hint | SCR_002762 | High-quality INTeractomes | 2026-08-06 09:25:42 | 306 | |||||
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Entrez Gene Resource Report Resource Website 1000+ mentions |
Entrez Gene (RRID:SCR_002473) | NCBI_Gene, NCBI Genen NCBI Entrez | database, data or information resource | Database for genomes that have been completely sequenced, have active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. Includes nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases. All entries follow NCBI's format for data collections. Content of Entrez Gene represents result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. Content is updated as new information becomes available. | gene, gene expression, gene location, gene map, gene prediction, genome, genome sequence analysis, phenotype, nomenclature, gene mapping, protein, genetic code, function, annotation, gold standard, bio.tools |
is used by: Animal QTLdb is used by: NIF Data Federation is used by: LIPID MAPS Proteome Database is used by: DisGeNET is used by: Nowomics is used by: Cytokine Registry is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: Vesiclepedia is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Rat Gene Symbol Tracker is related to: Gene Reference into Function is related to: Integrated Molecular Interaction Database is related to: Biomine is related to: SEGS is related to: STOP is related to: Coremine Medical is related to: Consensus CDS is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: Array Information Library Universal Navigator is related to: biomaRt has parent organization: NCBI works with: Open Regulatory Annotation Database |
PMID:17148475 PMID:21115458 |
Free, Freely available | nif-0000-02801, biotools:entrez_gene, OMICS_01651, r3d100010650 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene, https://bio.tools/entrez_gene, https://doi.org/10.17616/R3603S | SCR_002473 | NCBI Gene, Gene - Gene mapped phenotypes, Gene - Gene and mapped phenotypes, Gene Database, GeneID | 2026-08-06 09:25:40 | 2830 | |||||
|
DBTSS: Database of Transcriptional Start Sites Resource Report Resource Website 100+ mentions |
DBTSS: Database of Transcriptional Start Sites (RRID:SCR_002354) | DBTSS | database, data or information resource | Database of transcriptional start sites (TSSs) representing exact positions in the genome based on a unique experimentally validated TSS sequencing method, TSS Seq. A major part of human adult and embryonic tissues are covered. DBTSS contains 491 million TSS tag sequences collected from a total of 20 tissues and 7 cell cultures. Also integrated is generated RNA-seq data of subcellular- fractionated RNAs and ChIP Seq data of histone modifications, RNA polymerase II and several transcriptional regulatory factors in cultured cell lines. Also included is external epigenomic data, such as chromatin map of the ENCODE project. They associated those TSS information with public and original SNV data, in order to identify single nucleotide variations (SNVs) in the regulatory regions. | cdna, cdna library, transcriptional start site, transcriptome, transcriptome analysis, tss-seq, genome, adult human, embryonic, cell, rna-seq, subcellular, rna, chip seq data, histone modification, rna polymerase ii, transcriptional regulatory factor, cell line, single nucleotide variation, regulatory region, genetic valuation, transcriptional regulation, bio.tools, FASEB list |
is used by: Transcriptional Regulatory Element Database is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
Japan Society for the Promotion of Science ; Japanese Ministry of Education Culture Sports Science and Technology MEXT |
PMID:22086958 PMID:19910371 PMID:17942421 PMID:16381981 PMID:14681363 PMID:11752328 |
nif-0000-02738, biotools:dbtss, OMICS_01860 | https://bio.tools/dbtss | SCR_002354 | DBTSS: Database of Transcriptional Start Sites, DataBase of Transcriptional Start Sites | 2026-08-06 09:25:38 | 124 | |||||
|
RESID Resource Report Resource Website 10+ mentions |
RESID (RRID:SCR_003505) | RESID | database, data or information resource | A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. It provides: systematic and alternate names, atomic formulas and masses, enzyme activities generating the modifications, keywords, literature citations, Gene Ontology cross-references, Protein Information Resource (PIR) and SWISS-PROT protein sequence database feature table annotations, structure diagrams and molecular models. Each RESID Database entry presents a chemically unique modification and shows how that modification is currently annotated in the protein sequence databases, Swiss-Prot and the Protein Information Resource (PIR). The RESID Database provides a table of corresponding equivalent feature annotations that is used in the UniProt project, an international effort to combine the resources of the Swiss-Prot, TrEMBL and PIR. As an annotation tool, the RESID Database is used in standardizing and enhancing modification descriptions in the feature tables of Swiss-Prot entries. | protein cross-link, protein modification, protein structure, protein, structure, annotation, amino-terminal, carboxyl-terminal, peptide chain cross-link, post-translational modification, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:15174122 PMID:12520062 |
nif-0000-03400, r3d100000023, biotools:resid | https://bio.tools/resid, https://doi.org/10.17616/R3Z59M | http://www.ebi.ac.uk/RESID/ | SCR_003505 | RESID Database at the EBI, RESID Database at PIR, RESID Database of Protein Modifications, RESID Database | 2026-08-06 09:25:55 | 10 | |||||
|
GeneFisher Resource Report Resource Website 10+ mentions |
GeneFisher (RRID:SCR_003060) | GeneFisher, GeneFisher2 | data analysis service, production service resource, analysis service resource, service resource | A web-based program for designing degenerate primers. The procedure leads to isolation of genes in a target organism using multiple alignments of related genes from different organisms. The term gene fishing refers to the technique where PCR is used to isolate a postulated but unknown target sequence from a pool of DNA. | primer design, gene, degenerate primer, degenerate, primer, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:8877506 | Free, Freely available | biotools:genefisher, OMICS_02341 | https://bio.tools/genefisher | SCR_003060 | GeneFisher2 - Interactive PCR Primer Design | 2026-08-06 09:25:47 | 37 | |||||
|
IPI Resource Report Resource Website 50+ mentions |
IPI (RRID:SCR_003012) | IPI | database, data or information resource | IPI provides a top level guide to the main databases (UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, RefSeq, Ensembl, TAIR, H-InvDB, Vega) that describe the proteomes of higher eukaryotic organisms. IPI: :1. effectively maintains a database of cross references between the primary data sources :2. provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) :3. maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources. As previously announced, the closure of IPI has been proposed for some time. Replacement data sets are now available through UniProt for human and mouse; sets for the other species contained within IPI are expected to be included as part of the UniProt release 2011_07. To allow users time to transition to using the new UniProt data sets, IPI releases will continue to be produced throughout the summer. The final release will be made in September 2011. Thereafter, the IPI website will cease to be maintained, although previous releases of the dataset will continue to be available from the FTP site. We would like to thank our users for their support and interest in this service. | human, mouse, rat, zebrafish, arabidopsis, chicken, cow, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: UniProt DAS has parent organization: European Bioinformatics Institute works with: PremierBiosoft Proteo IQ Software |
PMID:15221759 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:ipi, nif-0000-03043 | https://bio.tools/ipi | SCR_003012 | International Protein Index, IPI - International Protein Index | 2026-08-06 09:25:46 | 76 | |||||
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IPD - Immuno Polymorphism Database Resource Report Resource Website 10+ mentions |
IPD - Immuno Polymorphism Database (RRID:SCR_003004) | IPD | database, data or information resource | A set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: * IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, * IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; * IPD-human platelet antigens, alloantigens expressed only on platelets and * IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterized melanoma cell lines. | polymorphic gene, immune system, gene, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
European Union contract QLRI-CT-200!-01325; NCI P01 111412 |
PMID:19875415 PMID:18449992 PMID:15608253 |
biotools:ipd, nif-0000-03038, r3d100010797 | https://bio.tools/ipd, https://doi.org/10.17616/R3KK7K | SCR_003004 | IPD-The Immuno Polymorphism Database, IPD - The Immuno Polymorphism Database | 2026-08-06 09:25:46 | 24 | |||||
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Gene Array Analyzer Resource Report Resource Website 1+ mentions |
Gene Array Analyzer (RRID:SCR_008323) | GAA | data analysis service, production service resource, analysis service resource, service resource | Data analysis service that allows to process CEL files from Affymetrix, Inc. GeneChip Gene 1.0 ST Arrays to identify alternative splicing. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22123740 | Acknowledgement requested | OMICS_00759, biotools:gene_array_analyzer | https://bio.tools/gene_array_analyzer | SCR_008323 | 2026-08-06 09:27:08 | 5 | ||||||
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PDB Finder Resource Report Resource Website 1+ mentions |
PDB Finder (RRID:SCR_008284) | PDB Finder | database, data or information resource | It is a very information rich protein structure database. Unfortunately, the PDB people are not very good at making their data available for search engines. There are several reasons why search engines often fail on the PDB: * The PDB has zillions of small administrative errors * The PDB-format is search-engine unfriendly * Many PDB files are incomplete The PDBFINDER project is a possible solution to these problems. The PDBFINDER holds for each PDB file a structured, search-engine-friendly-formatted entry that holds the data-items most likely needed for people search for certain types of PDB entries. The PDBFINDER is not useful to search in atomic coordinates; it is meant to ad searches in the administrative records of PDB files. Originally, the PDBFINDER was just for searching in PDB files. However, as all the time more people are using the PDBFINDER to aid modelling and database projects, they decided to also produce the so-called PDBFINDER2. The PDBFINDER2 also holds a lot of quality information about the PDB entries. Please only use the PDBFINDER2 if you really need that quality determination aspect because the PDBFINDER2 is five times bigger than the original PDBFINDER. | bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:pdbfinder, nif-0000-23902 | https://bio.tools/pdbfinder | SCR_008284 | 2026-08-06 09:27:07 | 1 | ||||||||
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SVM based method for predicting beta hairpin structures in proteins Resource Report Resource Website 1+ mentions |
SVM based method for predicting beta hairpin structures in proteins (RRID:SCR_008349) | data analysis service, production service resource, analysis service resource, service resource | Bhairpred server is based on machine learning technique SVM using single sequence information, evolutionary profile, predicted and observed secondary structure (as obtained using Psipred and DSSP), predicted and observed accessibility values (as obtainned from Netasa and DSSP). The methods were trained and tested on dataset of 2880 proteins and their performance was evaluated on dataset of 534 proteins used by Thornton (PNAS, 2002). Best prediction results were obtained with hybrid approach that combined prediction results from evolutionary profile, predicted secondary structure and accessibility. | evolutionary, information, protein, protein structure prediction, secondary, sequence, single, svm, technique, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Institute of Microbial Technology; Chandigarh; India |
Institute of Microbial Technology | nif-0000-25213, biotools:bhairpred | https://bio.tools/bhairpred | SCR_008349 | BhairPred | 2026-08-06 09:27:08 | 2 | |||||||
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ExpressYourself Resource Report Resource Website |
ExpressYourself (RRID:SCR_008881) | ExpressYourself | data analysis service, production service resource, analysis service resource, service resource | A fully integrated platform for processing microarray data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00755, biotools:expressyourself | https://bio.tools/expressyourself | SCR_008881 | ExpressYourself: microarray data processing platform, Express Yourself, Express Yourself: microarray data processing platform | 2026-08-06 09:27:13 | 0 | |||||||
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miRNEST Resource Report Resource Website 1+ mentions |
miRNEST (RRID:SCR_008907) | miRNEST | database, data or information resource | A database of animal, plant and virus microRNA data maintained at the University of Poznan. The database provides: * 9980 miRNA candiates from 420 animal and plant species predicted in Expressed Sequence Tags * predicted targets for plant candidates * RNA-seq reads mapped to candidates from 29 species * external data from 12 databases that includes sequences, polymorphism, expression and regulation. miRNEST 1.0, it contains miRNA from 563 animals, plants and viruses plant species. | microrna, expressed sequence tag, rna-seq read, sequence, polymorphism, mirna sequence, small rna sequence, single nucleotide polymorphism, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Adam Mickiewicz University in Poznan; Poznan; Poland |
European Social Fund ; Adam Mickiewicz University PBWB-08/2011; Polish Ministry of Science and Higher Education N N301 160935; Polish Ministry of Science and Higher Education N N516 441938 |
PMID:22135287 | nlx_151465, biotools:mirnest | http://mirnest.amu.edu.pl, https://bio.tools/mirnest | SCR_008907 | miRNEST - a database of animal and plant microRNAs | 2026-08-06 09:27:14 | 3 | |||||
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hiPathDB - human integrated Pathway DB with facile visualization Resource Report Resource Website 1+ mentions |
hiPathDB - human integrated Pathway DB with facile visualization (RRID:SCR_008900) | hiPathDB | database, data or information resource | hiPathDB is an integrated pathway database that combines the curated human pathway data of NCI-Nature PID, Reactome, BioCarta and KEGG. In total, it includes 1661 pathways consisting of 8976 distinct physical entities. (2010.03.09) hiPathDB provides two different types of integration. The pathway-level integration, conceptually a simple collection of individual pathways, was achieved by devising an elaborate model that takes distinct features of four databases into account and subsequently reformatting all pathways in accordance with our model. The entity-level integration creates a single unified pathway that encompasses all pathways by merging common components. Even though the detailed molecular-level information such as complex formation or post-translational modifications tends to be lost, such integration makes it possible to investigate signaling network over the entire pathways and allows identification of pathway cross-talks. Another strong merit of hiPathDB is the built-in pathway visualization module that supports explorative studies of complex networks in an interactive fashion. The layout algorithm is optimized for virtually automatic visualization of the pathways. | pathway, gene, compound, interaction, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: BioCarta Pathways is related to: Reactome is related to: Pathway Interaction Database has parent organization: Korea Research Institute of Bioscience and Biotechnology; Daejeon; South Korea |
Ewha Womans University; Seoul; Korea ; Korean Ministry of Education Science and Technology 2011-000232; Korean Ministry of Education Science and Technology 2011-0019745; Korean Ministry of Education Science and Technology R15-2006-020 |
PMID:22123737 | nlx_151413, biotools:hipathdb | https://bio.tools/hipathdb | SCR_008900 | Human Integrated Pathway Database | 2026-08-06 09:27:17 | 3 | |||||
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GFINDer: Genome Function INtegrated Discoverer Resource Report Resource Website 1+ mentions |
GFINDer: Genome Function INtegrated Discoverer (RRID:SCR_008868) | GFINDer | data analysis service, production service resource, analysis service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 16, 2019. Multi-database system providing large-scale lists of user-classified sequence identifiers with genome-scale biological information and functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves updated annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list, and calculates statistical significance values for each category. Moreover, GFINDer enables to functionally classify genes according to mined functional categories and to statistically analyze the obtained classifications, aiding in better interpreting microarray experiment results. | annotation, statistical analysis, mining, genome, function, sequence, functional profile, gene, microarray, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Polytechnic University of Milan; Milan; Italy |
PMID:15980570 PMID:15215397 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149256, biotools:gfinder | https://www.hsls.pitt.edu/obrc/index.php?page=URL1098209538, https://bio.tools/gfinder | SCR_008868 | Genome Function INtegrated Discoverer, Genome Function INtegrated Discoverer (GFINDer) | 2026-08-06 09:27:14 | 1 | |||||
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MicroSNiPer Resource Report Resource Website 10+ mentions |
MicroSNiPer (RRID:SCR_009880) | MicroSNiPer | data analysis service, production service resource, analysis service resource, service resource | A web-based application which predicts the impact of a SNP on putative microRNA targets. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: National Institute of Mental Health |
PMID:20809528 | biotools:microsniper, OMICS_00388 | https://bio.tools/microsniper | SCR_009880 | 2026-08-06 09:27:24 | 18 | |||||||
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Phylogeny.fr Resource Report Resource Website 500+ mentions |
Phylogeny.fr (RRID:SCR_010266) | database, data or information resource | A free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences. | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
PMID:18424797 | nlx_156923, biotools:phylogeny.fr | https://bio.tools/phylogeny.fr | SCR_010266 | 2026-08-06 09:27:30 | 667 | ||||||||
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mirTools Resource Report Resource Website 10+ mentions |
mirTools (RRID:SCR_009701) | mirTools | data analysis service, production service resource, analysis service resource, service resource | A comprehensive web server developed to allow researchers to comprehensively characterize small RNA transcriptome. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23778453 | OMICS_00365, biotools:mirtools | https://bio.tools/mirtools | SCR_009701 | mirTools 2.0 | 2026-08-06 09:27:19 | 13 | ||||||
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Hippocampome.org Resource Report Resource Website 10+ mentions |
Hippocampome.org (RRID:SCR_009023) | Hippocampome | database, data or information resource | A curated knowledge base of the circuitry of the hippocampus of normal adult, or adolescent, rodents at the mesoscopic level of neuronal types. Knowledge concerning dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex is distilled from published evidence and is continuously updated as new information becomes available. Each reported neuronal property is documented with a pointer to, and excerpt from, relevant published evidence, such as citation quotes or illustrations. Please note: This is an alpha-testing site. The content is still being vetted for accuracy and has not yet undergone peer-review. As such, it may contain inaccuracies and should not (yet) be trusted as a scholarly resource. The content does not yet appear uniformly across all combinations of browsers and screen resolutions. | interneuron, classification, neuroinformatics, network, hippocampus, neuron, property, morphology, molecular marker, electrophysiology, adult, adolescent, dentate gyrus, ca3, ca2, ca1, subiculum, entorhinal cortex, bio.tools |
is used by: BICCN is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: George Mason University; Virginia; USA |
Normal | Air Force Office of Scientific Research ; Office of Naval Research MURI N00014-10-1-0198; NINDS R01NS39600; NINDS R21NS58816 |
Except otherwise noted, Creative Commons Attribution-ShareAlike License | nlx_152892, biotools:Hippocampome.org | http://www.nitrc.org/projects/hippocampome, https://bio.tools/Hippocampome.org | SCR_009023 | Hippocampome Portal | 2026-08-06 09:27:16 | 32 | ||||
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T-Coffee Resource Report Resource Website 1000+ mentions |
T-Coffee (RRID:SCR_011818) | T-Coffee | data analysis service, production service resource, analysis service resource, service resource | A multiple sequence alignment server which can align Protein, DNA and RNA sequences. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:10964570 DOI:10.1006/jmbi.2000.4042 |
biotools:tcoffee, OMICS_00989 | https://bio.tools/tcoffee, https://sources.debian.org/src/t-coffee/ | SCR_011818 | T-Coffee: Aligns DNA RNA or Proteins using the default T-Coffee | 2026-08-06 09:27:49 | 1121 |
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