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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Mouse Genome Database Resource Report Resource Website 500+ mentions |
Mouse Genome Database (RRID:SCR_012953) | MGD | data or information resource, database | Community model organism database for laboratory mouse and authoritative source for phenotype and functional annotations of mouse genes. MGD includes complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics.Contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. | gene, genome, genetic, chromosome, clone, cytogenetic, dna, genomic, inbred, mammalian, mouse, mutant, ortholog, phenotype, primer, protein, reagent, sequence, strain, bio.tools |
is used by: DisGeNET is listed by: Debian is listed by: bio.tools is related to: Mouse Genome Informatics (MGI) has parent organization: Jackson Laboratory |
NHGRI HG000330 | PMID:21051359 | biotools:mgi, biotools:mgd, nif-0000-10301 | http://www.informatics.jax.org/mgihome/projects/overview.shtml, https://bio.tools/mgd, https://bio.tools/mgi | SCR_012953 | Mouse Genome Informatics: Mouse Genome Database, MGID, Mouse Genome Informatics Database | 2026-09-05 06:32:03 | 545 | |||||
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HOMD Resource Report Resource Website 100+ mentions |
HOMD (RRID:SCR_012770) | HOMD | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on April 14,2022. Database of comprehensive information on the approximately 600 prokaryote species that are present in the human oral cavity. The majority of these species are uncultivated and unnamed, recognized primarily by their 16S rRNA sequences. The HOMD presents a provisional naming scheme for the currently unnamed species so that strain, clone, and probe data from any laboratory can be directly linked to a stably named reference entity. The HOMD links sequence data with phenotypic, phylogenetic, clinical, and bibliographic information. Full and partial oral bacterial genome sequences determined as part of this project and the Human Microbiome Project, are being added to the HOMD as they become available. HOMD offers easy to use tools for viewing all publicly available oral bacterial genomes. Data is also downloadable. | taxon, genome, 16s rna, sequence, actinobacteria, bacteroidetes, chlamydiae, chloroflexi, euryarchaeota, firmicutes, fusobacteria, proteobacteria, spirochaetes, sr1, synergistetes, tenericutes, tm7, nomenclature, naming scheme, human, FASEB list | has parent organization: Forsyth Institute | NIDCR ; ARRA ; DOE contract U01 DE016937; DOE DE016937; DOE DE015847; DOE DE017106 |
PMID:20624719 PMID:20656903 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_22198, r3d100012898 | SCR_012770 | Human Oral Microbiome Database | 2026-09-05 06:32:02 | 137 | |||||
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SYFPEITHI: A Database for MHC Ligands and Peptide Motifs Resource Report Resource Website 100+ mentions |
SYFPEITHI: A Database for MHC Ligands and Peptide Motifs (RRID:SCR_013182) | SYFPEITHI | data or information resource, database | SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only. It contains a collection of MHC class I and class II ligands and peptide motifs of humans and other species, such as apes, cattle, chicken, and mouse, for example, and is continuously updated. Searches for MHC alleles, MHC motifs, natural ligands, T-cell epitopes, source proteins/organisms and references are possible. Hyperlinks to the EMBL and PubMed databases are included. In addition, ligand predictions are available for a number of MHC allelic products. The database is based on previous publications on T-cell epitopes and MHC ligands. It contains information on: -Peptide sequences -anchor positions -MHC specificity -source proteins, source organisms -publication references Since the number of motifs continuously increases, it was necessary to set up a database which facilitates the search for peptides and allows the prediction of T-cell epitopes. The prediction is based on published motifs (pool sequencing, natural ligands) and takes into consideration the amino acids in the anchor and auxiliary anchor positions, as well as other frequent amino acids. The score is calculated according to the following rules: The amino acids of a certain peptide are given a specific value depending on whether they are anchor, auxiliary anchor or preferred residue. Ideal anchors will be given 10 points, unusual anchors 6-8 points, auxiliary anchors 4-6 and preferred residues 1-4 points. Amino acids that are regarded as having a negative effect on the binding ability are given values between -1 and -3. Sponsors: SYFPEITHI is supported by DFG-Sonderforschungsbereich 685 and theEuropean Union: EU BIOMED CT95-1627, BIOTECH CT95-0263, and EU QLQ-CT-1999-00713. | epitope, allele, allelic, amino acid, ape, bind, cattle, chicken, class i, class ii, human, immunological database, ligand, mhc, molecule, motif, mouse, natural, organism, peptide, product, protein, sequence, specie, t-cell, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Tubingen; Tubingen; Germany |
nif-0000-21383, biotools:syfpeithi | https://bio.tools/syfpeithi | SCR_013182 | SYFPEITHI | 2026-09-05 06:32:04 | 269 | |||||||
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Therapeutically Relevant Multiple Pathways Database Resource Report Resource Website 1+ mentions |
Therapeutically Relevant Multiple Pathways Database (RRID:SCR_013471) | data or information resource, database | The Therapeutically Relevant Multiple Pathways Database is designed to provide information about such multiple pathways and related therapeutic targets described in the literatures, the targeted disease conditions, and the corresponding drugs/ligands directed at each of these targets. This database currently contains 11 entries of multiple pathways, 97 entries of individual pathways, 120 targets covering 72 disease conditions along with 120 sets of drugs directed at each of these targets. Each entry can be retrieved through multiple methods including multiple pathway name, individual pathway name and disease name. Additional information provided include protein name, synonyms, Swissprot AC number, species, gene name and location, protein sequence (AASEQ) and gene sequence (NTSEQ) as well as potential therapeutic implications while applicable. Cross-links to other databases are provided which include Genecard, GDB, Locuslink, NCBI, KEGG, OMIM, SwissProt to facilitate the access of more detailed information about various aspects of the particular target or non-target protein. Queries can be submitted by entering or selecting the required information in any one or combination of the fields in the form. User can specify full name or any part of the name in a text field, or choose one item from an selection field. Sponsors: TRMP is supported by the National University of Singapore. | drug, gene, condition, disease, intermolecular interactions and signaling pathways databases, ligand, literature, location, pathway, protein, sequence, specie, target, therapeutic, therapy | nif-0000-21402 | SCR_013471 | TRMP | 2026-09-05 06:32:07 | 3 | ||||||||||
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Manipulate and Display a DNA Sequence Resource Report Resource Website |
Manipulate and Display a DNA Sequence (RRID:SCR_013470) | Manipulate and Display a DNA Sequence | analysis service resource, data analysis service, production service resource, service resource | A software tool that allows users to input a DNA (or RNA) sequence and obtain its inverse, complement or inverse complement. The program can also be used to display a DNA sequence and its complement in double-stranded format. Functions after users paste a DNA sequence into the upper text box, then click the appropriate button to place a manipulated form of the sequence in the lower text box. | dna sequence, dna, rna, sequence, inverse, complement, inverse complement, base number | has parent organization: Colorado State University; Colorado; USA | nif-0000-31779 | SCR_013470 | Manipulate Display a DNA Sequence | 2026-09-05 06:32:07 | 0 | ||||||||
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Codon and Codon-Pair Usage Tables Resource Report Resource Website 1+ mentions |
Codon and Codon-Pair Usage Tables (RRID:SCR_018504) | CoCoPUTs | data or information resource, database | Database includes genomic codon-pair and dinucleotide statistics of all organisms with sequenced genome. Facilitates genetic variation analyses and recombinant gene design. Derived from all available GenBank and RefSeq data. | Codon-pair, codon, nucleotide, gene, genomic codon pair, dinucleotide statistic, sequence, genetic variation, recombinant gene design, data |
is related to: GenBank is related to: RefSeq |
PMID:31029701 | Free, Freely available | SCR_018504 | 2026-09-05 06:32:16 | 6 | ||||||||
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Database of Antimicrobial Activity and Structure of Peptides Resource Report Resource Website 50+ mentions |
Database of Antimicrobial Activity and Structure of Peptides (RRID:SCR_016600) | DBAASP | data or information resource, database | Collection of manually curated data regarding structure and antimicrobial activity of natural and synthetic peptides. Provides the information and analytical resources to develop antimicrobial compounds with the high therapeutic index. | data, collection, structure, antimicrobial, activity, natural, synthetic, peptide, sequence | International Science and Technology Center ; NIAID G2102; Shota Rustaveli National Science Foundation FR397718014 |
PMID:26578581 PMID:27060142 |
Free, Freely available | SCR_016600 | DataBase of Antimicrobial Activity and Structure of Peptides, Database of Antimicrobial Activity and Structure of Peptides | 2026-09-05 06:32:13 | 53 | |||||||
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RegulomeDB Resource Report Resource Website 100+ mentions |
RegulomeDB (RRID:SCR_017905) | data or information resource, database, service resource | Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature. | Annotate, SNP, regulatory, DNA, element, intergenic, region, human, genome, sequence, DNAase, hypersensitivity, binding, site, transcription, factor, promoter, region, data, FASEB list | Beta Cell Consortium ; NHGRI U54 HG 004558 |
PMID:22955989 | Free, Freely available | SCR_017905 | 2026-09-05 06:32:15 | 161 | |||||||||
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DREME Resource Report Resource Website 10+ mentions |
DREME (RRID:SCR_016860) | analysis service resource, data analysis service, production service resource, service resource | Software tool to discover short, ungapped motifs (recurring, fixed-length patterns) that are relatively enriched in sequences compared with shuffled sequences or control sequences (sample output from sequences). | discover, short, ungapped, motif, sequence, compare, shuffled, control, sample, output, recurring, fixed, length, pattern, data | is listed by: MEME Suite - Motif-based sequence analysis tools | Free, Available for download, Freely avaialble | SCR_016860 | Discriminative Regular Expression Motif Elicitation, DREME | 2026-09-05 06:32:14 | 23 | |||||||||
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seqNMF Resource Report Resource Website 1+ mentions |
seqNMF (RRID:SCR_017068) | data analysis software, data processing software, software application, software resource | Software tool for unsupervised discovery of sequential structure. Used to detect sequences in neural data generated by internal behaviors, such as animal thinking or sleeping. Used for unsupervised discovery of temporal sequences in high dimensional datasets in neuroscience without reference to external markers. | sequence, structure, high, dimention, dataset, neuroscience, repeated, sequential, pattern, data | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | Department of Energy ; Labor and Economic Growth Computational Science Graduate Fellowship ; G Harold and Leila Y. Mathers Foundation ; NIBIB T32 EB019940; NIDCD R01 DC009183; NIMH R25 MH062204; NINDS U19 NS10 4648; Simons Foundation Simons Collaboration for the Global Brain ; U.S. Department of Defense NDSEG Fellowship program |
PMID:30719973 | Free, Available for download, Freely available | SCR_017068 | 2026-09-05 06:28:18 | 6 | ||||||||
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rnaSPAdes Resource Report Resource Website 50+ mentions |
rnaSPAdes (RRID:SCR_016992) | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | 2026-09-05 06:28:16 | 58 | ||||||
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Clustal 2 Resource Report Resource Website 1000+ mentions |
Clustal 2 (RRID:SCR_017055) | alignment software, data processing software, data visualization software, image analysis software, software application, software resource | Software tool for nucleotide sequence alignment. Graphical version of multiple sequence alignment program for DNA and proteins. Windows interface for ClustalW multiple sequence alignment program. Provides integrated environment for performing multiple sequence and profile alignments and analyzing results. Available on Linux, Mac and Windows. | graphical, multiple, sequence, alignment, DNA, protein |
is related to: Clustal W2 is related to: Clustal Omega |
CNRS ; EMBL ; INSERM ; Ministère de la Recherche et Technologie ; Science Foundation Ireland |
PMID:17846036 PMID:9396791 |
Free, Available for download, Freely available | biotools:clustal2 | http://www.clustal.org/download/clustalx_help.html, https://bio.tools/clustal2 | SCR_017055 | Clustalx, CLUSTAL_X, clustalx, clustal X, clustal2 | 2026-09-05 06:28:17 | 1535 | |||||
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Nuclear Hormone Receptor Scan Resource Report Resource Website 1+ mentions |
Nuclear Hormone Receptor Scan (RRID:SCR_016975) | NHR-scan | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | 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 | Canadian Institutes of Health Research ; Pharmacia Corporation to the Center for Genomics and Bioinformatics |
PMID:15563547 | Free, Available, Acknowledgement requested | OMICS_14042 | SCR_016975 | NHR-scan, NHR Scan, NHRScan, Nuclear Hormoe Receptor Scan | 2026-09-05 06:28:16 | 5 | |||||
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EMBOSSMatcher Resource Report Resource Website 10+ mentions |
EMBOSSMatcher (RRID:SCR_017252) | alignment software, data access protocol, data processing software, image analysis software, software application, software resource, web service | Software tool for pairwise sequence alignment. Identifies local similarities in two input sequences. One of EMBL-EBI search and sequence analysis tools. | pairwise, sequence, alignment, identify, local, similarity, two, input, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools |
EMBL | PMID:30976793 | Free, Freely available | biotools:ebi_search | https://bio.tools/ebi_search | SCR_017252 | EMBOSS Matcher, emboss_matcher, EMBOSS_Matcher | 2026-09-05 06:28:21 | 16 | |||||
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Juicer Resource Report Resource Website 100+ mentions |
Juicer (RRID:SCR_017226) | data analysis software, data processing software, software application, software resource | Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps. | analysis, kilobase, resolution, Hi-C, data, terabase, dataset, transform, raw, sequence, normalized, contact, map | has parent organization: Baylor College of Medicine; Houston; Texas | Cancer Prevention Research Institute of Texas ; Google Research Award ; IBM University Challenge Award ; McNair Medical Institute Scholar Award ; NHGRI HG003067; NHGRI HG006193; NHLBI U01 HL130010; NIH Office of the Director DP2 OD008540; NSF PHY-1427654; NVIDIA Research Center Award ; PD Soros Fellowship ; President Early Career Award in Science and Engineering ; Welch Foundation |
PMID:27467249 | Free, Available for download, Freely available | SCR_017226 | 2026-09-05 06:28:20 | 119 | ||||||||
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PIRATE Resource Report Resource Website 10+ mentions |
PIRATE (RRID:SCR_017265) | data analysis software, data processing software, software application, software resource | Software pangenomics toolbox for clustering diverged orthologues in bacteria. Used to identify and classify orthologous gene families in bacterial pangenomes over wide range of sequence similarity thresholds. | Pangenome, clustering, genomics, bacteria, orthologue, gene, sequence, amino acid, nucleotide, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/598391 | Free, Available for download, Freely available | biotools:PIRAtE | https://bio.tools/PIRATE | SCR_017265 | Pangenome Iterative Refinement And Threshold Evaluation | 2026-09-05 06:28:21 | 23 | ||||||
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RepeatFiller Resource Report Resource Website 10+ mentions |
RepeatFiller (RRID:SCR_017414) | alignment software, data processing software, image analysis software, software application, software resource | Software tool to incorporate newly detected repeat overlapping alignments into pairwise alignment chains. It only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in chains, which makes it feasible to consider all seeds including those that overlap repetitive regions. Used to improve genome alignments by incorporating previously undetected local alignments between repetitive sequences. | Repeat, overlapping, alignment, pairwise, chain, local, genomic, region, colinear, block, sequence, undetected, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany |
DOI:10.1101/696922 | Free, Freely available | biotools:RepeatFiller, BioTools:RepeatFiller | https://bio.tools/RepeatFiller, https://bio.tools/RepeatFiller, https://bio.tools/RepeatFiller | SCR_017414 | 2026-09-05 06:28:24 | 16 | |||||||
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trimAl Resource Report Resource Website 500+ mentions |
trimAl (RRID:SCR_017334) | data analysis software, data processing software, software application, software resource | Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses. | removal, spurious, sequence, poorly, aligned, region, multiple, alignment, trimming, large, scale, phylogenetic, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
FIS ; MEC |
PMID:19505945 | Free, Available for download, Freely available | biotools:trimal | https://vicfero.github.io/trimal/, https://bio.tools/trimal | SCR_017334 | 2026-09-05 06:28:22 | 673 | ||||||
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HomoplasyFinder Resource Report Resource Website 1+ mentions |
HomoplasyFinder (RRID:SCR_017300) | data analysis software, data processing software, software application, software resource, software toolkit, standalone software | Software tool to identify and annotate homoplasies on phylogeny and sequence alignment. Used to automatically identify any homoplasies present in simulated and real phylogenetic data. Java application that can be used as standalone tool or within statistical programming environment R. | homoplasy, phylogeny, sequence, alignment, identify, data, annotate | Science Foundation Ireland | PMID:30663960 | Free, Available for download, Freely available | https://github.com/JosephCrispell/homoplasyFinder | SCR_017300 | 2026-09-05 06:28:22 | 6 | ||||||||
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BEAST2 Resource Report Resource Website 100+ mentions |
BEAST2 (RRID:SCR_017307) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager. | Bayesian, evolutionary, sampling, tree, phylogenic, analysis, Markov, chain, monte carlo, phylogenetic, population, genetic, phylodynamic, sequence |
is related to: BASTA is related to: BEAST is related to: PhyDyn has parent organization: University of Auckland; Auckland; New Zealand |
EMBL ; European Research Council ; Max Planck Society ; NIGMS U01 GM110749; Royal Society of New Zealand Marsden award ; Swiss National Science foundation |
PMID:30958812 | Free, Available for download, Freely available | SCR_017307 | , Beast 2.5 | 2026-09-05 06:28:22 | 211 |
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