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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GASV Resource Report Resource Website 1+ mentions |
GASV (RRID:SCR_000061) | GASV | software application, data processing software, data analysis software, software resource | Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions. | paired-end sequencing data, structural variant, probabilistic algorithm, discordant fragment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GASVPro has parent organization: Brown University; Rhode Island; USA |
Burroughs Wellcome Fund ; Department of Defense Breast Cancer Research ; ADVANCE Program at Brown University ; NSF 0548311 |
PMID:19477992 | Free, Available for download, Freely available | biotools:gasv, OMICS_01352 | http://compbio.cs.brown.edu/projects/gasv/ https://bio.tools/gasv |
SCR_000061 | Geometric Analysis of Structural Variants | 2026-02-15 09:17:51 | 4 | ||||
|
BAIT Resource Report Resource Website 1+ mentions |
BAIT (RRID:SCR_000511) | BAIT | software application, data visualization software, data processing software, software resource, data analysis software | Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data. | create strand inheritance plots, strand-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24028793 | Free, Available for download, Freely available | biotools:bait, OMICS_01531 | https://bio.tools/bait | SCR_000511 | BAIT - Software to help analyse Strand-Seq data | 2026-02-15 09:17:56 | 1 | |||||
|
Human Disease Ontology Resource Report Resource Website 1+ mentions |
Human Disease Ontology (RRID:SCR_000476) | DO | database, data or information resource, ontology, controlled vocabulary | Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases. | obo, pathological, organismal, cellular, disease, biomedical, health, neurologic disease, neurological disorder, phenotype, bio.tools, |
is used by: DOAF is listed by: BioPortal is listed by: OBO is listed by: bio.tools is listed by: Debian is related to: PharmGKB Ontology is related to: GWASdb is related to: NUgene Project is related to: FunDO is related to: Neurocarta has parent organization: University of Maryland School of Medicine; Maryland; USA |
NHGRI U24 HG012557 | PMID:22080554 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-35926, nlx_157432, SCR_003491, biotools:disease_ontology | http://disease-ontology.org/ https://bio.tools/disease_ontology http://purl.obolibrary.org/obo/doid.obo |
http://do-wiki.nubic.northwestern.edu/index.php/Main_Page | SCR_000476 | Human Disease Ontology Knowledgebase, Disease Ontology | 2026-02-15 09:17:56 | 5 | |||
|
MPscan Resource Report Resource Website |
MPscan (RRID:SCR_000587) | MPscan | web service, data access protocol, software resource | Web tool for index free mapping of multiple short reads on a genome. | linux, macos, next-generation sequencing, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: ATGC: Montpellier bioinformatics platform |
Free, Available for download, Freely available | biotools:mpscan, OMICS_00670 | https://bio.tools/mpscan | SCR_000587 | MPscan: index free mapping of multiple short reads on a genome | 2026-02-15 09:17:57 | 0 | ||||||
|
STAR Resource Report Resource Website 10000+ mentions |
STAR (RRID:SCR_004463) | software application, data processing software, software resource, alignment software, image analysis software | Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays. | RNA-seq data, alignment, RNA-seq reads alignment, reference genome, using uncompressed suffix arrays, bio.tools |
is used by: STARsolo is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
NHGRI U54 HG004557 | PMID:23104886 DOI:10.1093/bioinformatics/bts635 |
biotools:star, OMICS_01254, SCR_015899 | https://github.com/alexdobin/STAR https://bio.tools/star https://sources.debian.org/src/rna-star/ |
SCR_004463 | Spliced Transcripts Alignment to Reference, Spliced Transcripts Alignment to a Reference (STAR), rna-star, ultrafast universal RNA-seq aligner | 2026-02-15 09:18:43 | 22809 | ||||||
|
TAGS Resource Report Resource Website 100+ mentions |
TAGS (RRID:SCR_004294) | TAGS | software application, time-series analysis software, data processing software, software resource, data analysis software | Software tool for gene set enrichment analysis for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations. The installation file is for Windows., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, enrichment analysis, time series, function, structure, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Tsinghua University; Beijing; China |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tags, nlx_31187 | https://bio.tools/tags | http://166.111.130.26/member/yliu/TAGS/ | SCR_004294 | 2026-02-15 09:18:40 | 139 | ||||||
|
neurodebian Resource Report Resource Website 10+ mentions |
neurodebian (RRID:SCR_004401) | NeuroDebian | software application, source code, data processing software, software resource, software development tool, data distribution software, software development environment, software repository | Collection based on a collaborative effort of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives. Popular packages include AFNI, FSL, PyMVPA and many others. It contains both unofficial or prospective packages which are not (yet) available from the main Debian archive, as well as backported or simply rebuilt packages also available elsewhere. A listing of current and planned projects is available if you want to get involved. The main goal of the project is to provide a versatile and convenient environment for neuroscientific research that is based on open-source software. To this end, the project offers a package repository that complements the main Debian (and Ubuntu) archive. NeuroDebian is not yet another Linux distribution, but rather an effort inside the Debian project itself. Software packages are fully integrated into the Debian system and from there will eventually migrate into Ubuntu as well. With NeuroDebian, installing and updating neuroscience software is no different from any other part of the operating system. Maintaining a research software environment becomes as easy as installing an editor. There is also virtual machine to test NeuroDebian on Windows or Mac OS. If you want to see your software packaged for Debian, please drop them a note. | linux, linux distribution, virtual machine, fmri, eeg, pymvpa, python, r, debian, brain image, neuroscience, platform, afni brik, bshort, bfloat, console (text based), dicom, domain independent, freebsd, gnome, kde, linux, minc2, nifti, philips par/rec, development environment, posix/unix-like, system administrator, web environment |
lists: MRIcron is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ITK-SNAP is related to: NITRC Computational Environment is related to: PyMVPA is related to: MRtrix has parent organization: Debian has parent organization: Dartmouth College; New Hampshire; USA has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany is parent organization of: VoxBo is parent organization of: Computational Morphometry Toolkit |
PMID:23055966 | GNU General Public License v3, The community can contribute to this resource | nlx_143723 | http://www.nitrc.org/projects/neurodebian | SCR_004401 | Debian Neuroscience Repository, neuro debian | 2026-02-15 09:18:43 | 40 | |||||
|
BSRD Resource Report Resource Website 10+ mentions |
BSRD (RRID:SCR_004249) | BSRD | database, service resource, storage service resource, data repository, data or information resource | A repository for bacterial small regulatory RNA. They welcome you to submit new experimental validated sRNA targets. | srna target, srna, small regulatory non-coding rna, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:23203879 | Acknowledgement requested, The community can contribute to this resource | biotools:bsrd, OMICS_01533 | https://bio.tools/bsrd | SCR_004249 | BSRD - Bacterial Small Regulatory RNA Database, Bacterial Small Regulatory RNA Database | 2026-02-15 09:18:40 | 29 | |||||
|
NCBI BioSystems Database Resource Report Resource Website 100+ mentions |
NCBI BioSystems Database (RRID:SCR_004690) | BioSystems | data analysis service, database, service resource, storage service resource, production service resource, data repository, data or information resource, analysis service resource | Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them. | pathway, disease, gene, protein, small molecule, literature, computation, image, biomarker, drug, structural complex, functional set, biological system, molecule, gold standard, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: NCBI Structure is related to: BioCyc is related to: EcoCyc is related to: MetaCyc is related to: Reactome is related to: Pathway Interaction Database is related to: WikiPathways is related to: Gene Ontology has parent organization: NCBI |
NIH | PMID:19854944 | r3d100011033, biotools:biosystems, nlx_69646 | https://bio.tools/biosystems https://doi.org/10.17616/R31K80 |
SCR_004690 | BioSystems Database, NCBI BioSystems | 2026-02-15 09:18:47 | 118 | |||||
|
QuickGO Resource Report Resource Website 500+ mentions |
QuickGO (RRID:SCR_004608) | QuickGO | database, ontology, software resource, data access protocol, web service, data or information resource, controlled vocabulary | A web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at the EBI. It is able to offer a range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. The software for QuickGO is freely available under the Apache 2 license. QuickGO can supply GO term information and GO annotation data via REST web services. | gene, ontology, annotation, browser, visualization, search engine, slimmer-type tool, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, windows, mac os x, linux, unix, gold standard, bio.tools |
is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: STRAP has parent organization: European Bioinformatics Institute |
BBSRC BB/E023541/1 | PMID:19744993 PMID:20157483 |
Apache License, v2, Free for academic use | biotools:quickgo, nlx_60318, OMICS_02276 | https://bio.tools/quickgo | SCR_004608 | Quick GO | 2026-02-15 09:18:51 | 523 | ||||
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Small Molecule Pathway Database Resource Report Resource Website 50+ mentions |
Small Molecule Pathway Database (RRID:SCR_004844) | SMPDB | data analysis service, database, service resource, image, production service resource, data or information resource, analysis service resource | An interactive, visual database containing more than 350 small molecule pathways found in humans. More than 2/3 of these pathways (>280) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing exquisitely detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the HMDB or DrugBank and each protein or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. The database is easily browsed and supports full text, sequence and chemical structure searching. Users may query SMPDB with lists of metabolite names, drug names, genes / protein names, SwissProt IDs, GenBank IDs, Affymetrix IDs or Agilent microarray IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams. Gene, metabolite and protein concentration data can also be visualized through SMPDB''s mapping interface. All of SMPDB''s images, image maps, descriptions and tables are downloadable. | metabolomics, transcriptomics, proteomics, systems biology, small molecule, pathway, human, metabolic pathway, metabolic disease pathway, metabolite signaling pathway, drug-action pathway, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: ConsensusPathDB has parent organization: University of Alberta; Alberta; Canada |
Genome Alberta ; Genome Canada |
PMID:19948758 | nlx_143926, biotools:smpdb, r3d100012753 | https://bio.tools/smpdb https://doi.org/10.17616/R3TB93 |
SCR_004844 | SMPDB (The Small Molecule Pathway Database), Small Molecule Pathway Database (SMPDB) | 2026-02-15 09:18:50 | 95 | |||||
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ANTS - Advanced Normalization ToolS Resource Report Resource Website 100+ mentions |
ANTS - Advanced Normalization ToolS (RRID:SCR_004757) | ANTS | software application, data processing software, software resource, registration software, segmentation software, image analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Software package designed to enable researchers with advanced tools for brain and image mapping. Many of the ANTS registration tools are diffeomorphic*, but deformation (elastic and BSpline) transformations are available. Unique components of ANTS include multivariate similarity metrics, landmark guidance, the ability to use label images to guide the mapping and both greedy and space-time optimal implementations of diffeomorphisms. The symmetric normalization (SyN) strategy is a part of the ANTS toolkit as is directly manipulated free form deformation (DMFFD). *Diffeomorphism: a differentiable map with differentiable inverse. In general, these maps are generated by integrating a time-dependent velocity field. ANTS Applications: * Gray matter morphometry based on the jacobian and/or cortical thickness. * Group and single-subject optimal templates. * Multivariate DT + T1 brain templates and group studies. * Longitudinal brain mapping -- special similarity metric options. * Neonatal and pediatric brain segmentation. * Pediatric brain mapping. * T1 brain mapping guided by tractography and connectivity. * Diffusion tensor registration based on scalar or connectivity data. * Brain mapping in the presence of lesions. * Lung and pulmonary tree registration. * User-guided hippocampus labeling, also of sub-fields. * Group studies and statistical analysis of cortical thickness, white matter volume, diffusion tensor-derived metrics such as fractional anisotropy and mean diffusion., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | algorithm, atlas application, morphology, segmentation, image registration, temporal transformation, child, pediatric, normalization |
is used by: CMIND PY is used by: BICCN is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: Segmentation of Hippocampus Subfields is related to: ANTsR has parent organization: University of Pennsylvania; Philadelphia; USA |
NIBIB R01 EB006266 | PMID:20851191 PMID:33907199 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_75959 | http://www.nitrc.org/projects/ants https://sources.debian.org/src/ants/ |
SCR_004757 | Advanced Normalization Tools | 2026-02-15 09:18:48 | 472 | ||||
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NCBI Probe Resource Report Resource Website 10+ mentions |
NCBI Probe (RRID:SCR_004816) | NCBI Probe | database, service resource, storage service resource, data repository, data or information resource | Public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications including genotyping, gene expression studies, SNP discovery, genome mapping, and gene silencing. Probe records contain information on reagent distributors, probe effectiveness, and computed sequence similarities. The database is constantly updated, with over 11,000,000 probes available. Users may deposit their data into NCBI Probe Database. | reagent, probe, registry, nucleic acid, gene expression, gene mapping, gene silencing, dna data bank, nucleic acid probe, gold standard, bio.tools |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: UniSTS has parent organization: NCBI |
Public, The community can contribute to this resource | nlx_80513, r3d100010780, biotools:ncbi_dbprobe | http://www.ncbi.nlm.nih.gov/sites/entrez?db=probe https://bio.tools/ncbi_dbprobe https://doi.org/10.17616/R3D041 |
SCR_004816 | NCBI Probe Database, Entrez Probe Database, ProbeDB, Probe Database, dbProbe | 2026-02-15 09:18:49 | 17 | ||||||
|
European Genome phenome Archive Resource Report Resource Website 500+ mentions |
European Genome phenome Archive (RRID:SCR_004944) | EGA | data set, software resource, data access protocol, web service, service resource, storage service resource, data repository, data or information resource | Web service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The repository allows you to explore datasets from numerous genotype experiments, supplied by a range of data providers. The EGA''s role is to provide secure access to the data that otherwise could not be distributed to the research community. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. As an example, only members of the EGA team are allowed to process data in a secure computing facility. Once processed, all data are encrypted for dissemination and the encryption keys are delivered offline. The EGA also supports data access only for the consortium members prior to publication. | phenomenon, trait, sequence, genotype, experiment, case-control, population, family study, snp, cnv, phenotype, genomic, gold standard, bio.tools |
is used by: Blueprint Epigenome is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
PMID:34791407 | Restricted | BioTools:ega, biotools:ega, r3d100011242, OMICS_01028, nlx_91316 | https://ega-archive.org/ https://bio.tools/ega https://bio.tools/ega https://doi.org/10.17616/R3W619 |
SCR_004944 | , The European Genome-phenome Archive, The European Genome-phenome Archive (EGA), EGA | 2026-02-15 09:18:52 | 605 | |||||
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Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets Resource Report Resource Website 1000+ mentions |
Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets (RRID:SCR_005040) | data or information resource, database, software resource | Percolator post-processes the results of a shotgun proteomics database search program, re-ranking peptide-spectrum matches so that the top of the list is enriched for correct matches. Shotgun proteomics uses liquid chromatography-tandem mass spectrometry to identify proteins in complex biological samples. We describe an algorithm, called Percolator, for improving the rate of peptide identifications from a collection of tandem mass spectra. Percolator uses semi-supervised machine learning to discriminate between correct and decoy spectrum identifications, correctly assigning peptides to 17% more spectra from a tryptic dataset and up to 77% more spectra from non-tryptic digests, relative to a fully supervised approach. The yeast-01 data is available in tab delimetered format. The SEQUEST parameter file and target database for the yeast and worm data are also available. | worm, yeast, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA |
PMID:17952086 | biotools:percolator, nlx_98814 | https://bio.tools/percolator | SCR_005040 | Percolator | 2026-02-15 09:18:53 | 2482 | |||||||
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SINA Resource Report Resource Website 100+ mentions |
SINA (RRID:SCR_005067) | SINA | data analysis service, software resource, service resource, production service resource, analysis service resource | Service to align and optionally taxonomically classify your rRNA gene sequences. The results can be combined with any other sequences aligned by SINA or taken from the SILVA databases by concatenation of FASTA files or using the ARB MERGE tool. Note: Submission is currently limited to at most 1000 sequences of at most 6000 bases each. If your requirements exceed this limitation, get Opens internal link in current windowSINA for local installation. | alignment, taxonomic classification, rrna, gene sequence, fasta, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SILVA is related to: ARB project has parent organization: Max Planck Institute for Marine Microbiology; Bremen; Germany |
PMID:22556368 | Free, Available for download, Freely available | OMICS_01438, biotools:sina | https://bio.tools/sina https://sources.debian.org/src/sina/ https://github.com/epruesse/SINA |
SCR_005067 | SINA Alignment Service, SILVA Incremental Aligner | 2026-02-15 09:18:54 | 369 | |||||
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PAZAR Resource Report Resource Website 10+ mentions |
PAZAR (RRID:SCR_005410) | PAZAR | database, software resource, service resource, storage service resource, data repository, data or information resource | Database that unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ''boutiques'' within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor, target gene, regulatory sequence, transcription factor profile, annotation, sequence, profile, transcription factor binding profile, chip, chip-seq, gene, cis-regulatory element, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of British Columbia; British Columbia; Canada has parent organization: SourceForge |
PMID:18971253 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00540, biotools:pazar | https://bio.tools/pazar | SCR_005410 | 2026-02-15 09:19:05 | 32 | ||||||
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TIGRFAMS Resource Report Resource Website 100+ mentions |
TIGRFAMS (RRID:SCR_005493) | JCVI TIGRFAMS, TIGRFAM | data or information resource, data set, database | Consists curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. Starting with release 10.0, TIGRFAMs models use HMMER3, which provides excellent search speed as well as exquisite search sensitivity. See the "TIGRFAMs Complete Listing" page to review the accession, protein name, model type, and EC number (if assigned) of all models. TIGRFAMs is a member database in InterPro. The HMM libraries and supporting files are available to download and use for free from our FTP site. | sequence alignment, hidden markov model, protein sequence, classification, protein, protein family, sequence homology, sequence, homology, function, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: InterPro is related to: InterPro has parent organization: J. Craig Venter Institute |
PMID:23197656 | Free | nif-0000-03560, OMICS_01700, biotools:tigrfams | https://bio.tools/tigrfams | http://www.tigr.org/TIGRFAMs | SCR_005493 | TIGRFAMs | 2026-02-15 09:18:59 | 135 | ||||
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Hmmer Resource Report Resource Website 5000+ mentions |
Hmmer (RRID:SCR_005305) | HMMER | software application, data analysis service, data processing software, software resource, service resource, production service resource, analysis service resource, data analysis software | Tool for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. | homolog, protein sequence, source code, FASEB list |
is used by: Mantis is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: SoftCite is related to: VectorBase has parent organization: Janelia Research |
Howard Hughes Medical Institute | PMID:21593126 DOI:10.1093/bioinformatics/14.9.755 |
OMICS_00996, nlx_144358 | https://sources.debian.org/src/hmmer/ | SCR_005305 | HMMER - biosequence analysis using profile hidden Markov models | 2026-02-15 09:18:56 | 8774 | |||||
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becas Resource Report Resource Website 10+ mentions |
becas (RRID:SCR_005337) | web service, data access protocol, service resource, software resource | Web application, API and widget able to recognize and annotate biomedical concepts in text.Provides annotations for isolated, nested and intersected entities.Identifies concepts from multiple semantic groups, providing preferred names and enriching them with references to public knowledge resources. | Annotation, biomedical concept recognition, annotate biomedical concepts, text, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Aveiro; Aveiro; Portugal |
Free, Freely available | biotools:becas, OMICS_01173 | https://bioinformatics.ua.pt/software/becas/ https://bio.tools/becas |
SCR_005337 | 2026-02-15 09:18:56 | 12 |
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