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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ImaGene Resource Report Resource Website 100+ mentions |
ImaGene (RRID:SCR_002178) | software resource, data processing software, software application, data analysis software | Software tool as convolutional neural network to quantify natural selection from genomic data.Supervised machine learning algorithm to predict natural selection and estimate selection coefficients from population genomic data. Can be used to estimate any parameter of interest from evolutionary population genetics model., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microarray analysis, machine vision, convolutional neural network, quantify natural selection, genomic data, population genomic data, evolutionary population, genetics model, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Imperial College London ; Politecnico di Milano |
PMID:31757205 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:ImaGene, OMICS_00841 | https://github.com/mfumagalli/ImaGene, https://bio.tools/ImaGene | http://www.biodiscovery.com/software/imagene/ | SCR_002178 | 2026-08-05 10:43:34 | 405 | |||||
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QualitySNPng Resource Report Resource Website 1+ mentions |
QualitySNPng (RRID:SCR_002479) | data processing software, software application, data visualization software, standalone software, software resource | Software for the detection and visualization of single nucleotide polymorphisms (SNPs) from next generation sequencing data that uses a haplotype-based strategy. | single nucleotide polymorphism, haplotype strategy, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23632165 | Free, Available for download, Freely available | biotools:qualitysnpng, OMICS_00070 | https://bio.tools/qualitysnpng | SCR_002479 | 2026-08-05 10:43:39 | 6 | |||||||
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VIRsiRNAdb Resource Report Resource Website 1+ mentions |
VIRsiRNAdb (RRID:SCR_006108) | VIRsiRNAdb | data or information resource, data repository, storage service resource, database, data analysis service, production service resource, service resource, analysis service resource | VIRsiRNAdb is a curated database of experimentally validated viral siRNA / shRNA targeting diverse genes of 42 important human viruses including influenza, SARS and Hepatitis viruses. Submissions are welcome. Currently, the database provides detailed experimental information of 1358 siRNA/shRNA which includes siRNA sequence, virus subtype, target gene, GenBank accession, design algorithm, cell type, test object, test method and efficacy (mostly quantitative efficacies). Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. The database has facilities like search, advance search (using Boolean operators AND, OR) browsing (with data sorting option), internal linking and external linking to other databases (Pubmed, Genbank, ICTV). Additionally useful siRNA analysis tools are also provided e.g. siTarAlign for aligning the siRNA sequence with reference viral genomes or user defined sequences. virsiRNAdb would prove useful for RNAi researchers especially in siRNA based antiviral therapeutics development. | virus, sirna, shrna, gene, influenza, sars, hepatitis, sirna sequence, virus subtype, target gene, genbank accession, design algorithm, cell type, efficacy, target genome region, target object, experimental assay, off-target, sirna matching, reference viral sequence, influenza virus, hepatitis b virus, hpv, sars corona virus, viral genome, reference genome, align, sirna sequence, fasta, blast, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Institute of Microbial Technology; Chandigarh; India |
Influenza, SARS, Hepatitis, Infectious disease | Council of Scientific and Industrial Research; New Delhi; India | PMID:22139916 | Open unspecified license / Freely available | nlx_151610, biotools:virsirnadb | https://bio.tools/virsirnadb | SCR_006108 | VIRsiRNAdb - Database of Viral siRNA / shRNA, Viral siRNA Database, Viral siRNA Database (VIRsiRNAdb) | 2026-08-05 10:44:25 | 4 | |||
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qrqc Resource Report Resource Website 1+ mentions |
qrqc (RRID:SCR_006867) | qrqc | data processing software, software application, sequence analysis software, data analysis software, software resource | Software R package to quickly scan reads and gather statistics on base and quality frequencies, read length, k-mers by position, and frequent sequences. Produces graphical output of statistics for use in quality control pipelines, and an optional HTML quality report. S4 SequenceSummary objects allow specific tests and functionality to be written around the data collected. | Quickly scan reads, read length, k-mers, position, frequent sequences, quality control pipeline, HTML quality report, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:qrqc, OMICS_01071 | https://github.com/vsbuffalo/qrqc, https://bio.tools/qrqc | SCR_006867 | quick read quality control, Quick Read Quality Control | 2026-08-05 10:44:33 | 2 | ||||||
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SPM Resource Report Resource Website 5000+ mentions Issue |
SPM (RRID:SCR_007037) | SPM | data processing software, image analysis software, software application, data analysis software, software resource | Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG. | analysis, brain, imaging, data, sequence, fMRI, PET, SPECT, EEG, MEG, bio.tools |
uses: Neuroimaging Data Model uses: imcalc: SPM batch image calculator is used by: rsfMRI_fconn calculation is used by: Automatic Analysis is used by: auto_acpc_reorient is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: SoftCite is affiliated with: Clinical Toolbox for SPM is affiliated with: Statistical non-Parametric Mapping is related to: WFU Biological Parametric Mapping Toolbox is related to: vis: SPM Visualized Statistics toolbox is related to: LEAD-DBS is related to: CCHMC Pediatric Brain Templates is related to: IBMA toolbox is related to: ArtRepair for robust fMRI is related to: ASL data processing tool box is related to: BrainVISA / Anatomist is related to: MRIcro Software is related to: xjView: A Viewing Program For SPM is related to: BrainMagix SPM Viewer is related to: MarsBaR region of interest toolbox for SPM is related to: NIRS-SPM is related to: SPM SS - fMRI functional localizers is related to: Wisconsin White Matter Hyperintensities Segmentation Toolbox is related to: Dementia-specific FDG PET Template for SPM analyses is related to: SPM Anatomy Toolbox is related to: MIPAV: Medical Image Processing and Visualization is related to: MATLAB is related to: hMRI-toolbox is related to: Sandwich Estimator Toolbox has parent organization: University College London; London; United Kingdom is required by: MRTool provides: TSDiffAna has plug in: ICN_Atlas works with: UManitoba - JHU Functionally Defined Human White Matter Atlas works with: NIAG Addiction Data works with: ICN_Atlas works with: spm_auto_reorient_coregister works with: Computational Anatomy Toolbox for SPM works with: FieldTrip works with: POAS4SPM |
Free, Available for download, Freely available | biotools:SPM | https://github.com/spm/spm12, https://bio.tools/SPM | https://www.fil.ion.ucl.ac.uk/spm/ | SCR_007037 | Statistical Parametric Mapping, SPM5, SPM2, SPM12, Statistical Parametric Mapping Software, SPM99, SPM8, SPM, SPM96 | 2026-08-05 10:44:35 | 8694 | |||||
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SoyBase Resource Report Resource Website 500+ mentions |
SoyBase (RRID:SCR_005096) | SoyBase | data or information resource, data repository, controlled vocabulary, storage service resource, database, data analysis service, ontology, production service resource, service resource, analysis service resource | Professionally curated repository for genetics, genomics and related data resources for soybean that contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase includes annotated Williams 82 genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. The repository maintains controlled vocabularies for soybean growth, development, and traits that are linked to more general plant ontologies. Contributions to SoyBase or the Breeder''s Toolbox are welcome. | soybean, gene, genetic map, genome, data set, trait, phenotype, molecular biology, sequence, chromosome, quantitative trait locus, php, genetics, genomics, legume, bio.tools, FASEB list |
is listed by: 3DVC is listed by: re3data.org is listed by: Debian is listed by: bio.tools has parent organization: Iowa State University; Iowa; USA is parent organization of: Soybean Ontologies is parent organization of: Soy Ontology |
USDA Agricultural Research Service | PMID:20008513 | The community can contribute to this resource | nif-0000-03483, r3d100010846, biotools:soybase | https://bio.tools/soybase, https://doi.org/10.17616/R3S032 | SCR_005096 | SoyBase and the Soybean Breeder''s Toolbox, SoyBase and the Soybean Breeder''s Toolbox: Integrating Genetics and Molecular Biology for Soybean Researchers | 2026-08-05 10:44:10 | 646 | ||||
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Generic GO Term Mapper Resource Report Resource Website 10+ mentions |
Generic GO Term Mapper (RRID:SCR_005806) | GOTermMapper, GO Term Mapper | data processing software, software application, software resource, data analysis service, production service resource, service resource, analysis service resource | The Generic GO Term Mapper finds the GO terms shared among a list of genes from your organism of choice within a slim ontology, allowing them to be binned into broader categories. The user may optionally provide a custom gene association file or slim ontology, or a custom list of slim terms. The implementation of this Generic GO Term Mapper uses map2slim.pl script written by Chris Mungall at Berkeley Drosophila Genome Project, and some of the modules included in the GO-TermFinder distribution written by Gavin Sherlock and Shuai Weng at Stanford University, made publicly available through the GMOD project. GO Term Mapper serves a different function than the GO Term Finder. GO Term Mapper simply bins the submitted gene list to a static set of ancestor GO terms. In contrast, GO Term Finder finds the GO terms significantly enriched in a submitted list of genes. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene ontology, gene, gene association, slim ontology, slimmer-type tool, term enrichment, gene annotation, genomics, ontology, process, function, component, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Generic Model Organism Database Project has parent organization: Princeton University; New Jersey; USA |
Free for academic use | nlx_149294, biotools:go_term_mapper | https://bio.tools/go_term_mapper | SCR_005806 | Generic Gene Ontology Term Mapper, Generic Gene Ontology (GO) Term Mapper | 2026-08-05 10:44:20 | 44 | ||||||
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SOURCE Resource Report Resource Website 50+ mentions |
SOURCE (RRID:SCR_005799) | SOURCE | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool | genomic, functional annotation, ontology, gene expression, gene, genome, statistical analysis, bio.tools, FASEB list |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: SMD |
NIGMS ; NCI CA85129-04; NIGMS GM07365 |
PMID:12519986 | Restricted | biotools:source, nlx_149287 | https://login.stanford.edu/idp/profile/SAML2/Redirect/SSO?execution=e1s1, https://bio.tools/source | SCR_005799 | 2026-08-05 10:44:21 | 69 | |||||
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SEECER Resource Report Resource Website 10+ mentions |
SEECER (RRID:SCR_005274) | SEECER | data processing software, algorithm resource, software application, data analysis software, sequence analysis software, software resource | Algorithm for sequencing error correction of RNA-seq data sets. SEECER removes mismatch and indel errors from the raw reads and improves downstream analysis of the data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Carnegie Mellon University; Pennsylvania; USA |
PMID:23558750 | Free, Available for download | OMICS_01236, biotools:seecer | https://bio.tools/seecer | SCR_005274 | SEECER - SEquencing Error CorrEction for Rna reads | 2026-08-05 10:44:12 | 12 | |||||
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IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature Resource Report Resource Website 10+ mentions |
IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature (RRID:SCR_006027) | IDEAL | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature, is a collection of knowledge on experimentally verified intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). IDEAL contains manually curated annotations on IDPs in locations, structures, and functional sites such as protein binding regions and posttranslational modification sites together with references and structural domain assignments. Protean segment One of the unique phenomena seen in IDPs is so-called the coupled folding and binding, where a short flexible segment can bind to its binding partner with forming a specific structure to act as a molecular recognition element. IDEAL explicitly annotates these regions as protean segment (ProS) when unstructured and structured information are both available in the region. Access to the data All the entries are tabulated in the list and individual entries can be retrieved by using the search tool at the upper-right corner in this page. IDEAL also provides the BLAST search, which can find homologs in IDEAL. All the information in IDEAL can be downloaded in the XML file. | intrinsically disordered protein, protein, intrinsically disordered region, region, location, structure, functional site, protein binding region, binding region, posttranslational modification site, reference, structural domain assignment, blast, homolog, simian virus 40, epstein-barr virus, human herpesvirus 1, residue, protean segment, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Nagoya University; Nagoya; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:22067451 | biotools:ideal, nlx_151427 | https://bio.tools/ideal | SCR_006027 | IDEAL - Intrinsically Disordered proteins with Extensive Annotations Literature, Intrinsically Disordered proteins with Extensive Annotations and Literature | 2026-08-05 10:44:25 | 10 | |||||
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Pathbase Resource Report Resource Website 10+ mentions |
Pathbase (RRID:SCR_006141) | Pathbase | image repository, data or information resource, data repository, controlled vocabulary, data access protocol, image collection, database, software resource, storage service resource, ontology, service resource, web service | Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development) | histopathology, photomicrograph, macroscopic, mutant, genetically manipulated, pathology, transgenic, rodent, mpath ontology, mouse pathology ontology, skinbase, genotype, skin, gene, tissue, hair, mutant mouse strain, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: University of Cambridge; Cambridge; United Kingdom is parent organization of: Mouse Pathology Ontology |
Lesion, Mutant mouse strain, Inbred mouse strain | North American Hair Research Society ; Ellison Medical Foundation ; European Union QLRI-1999-00320; European Union LSHG-CT-2006-037188; NCI CA089713; NCRR RR17436; NIH AR49288 |
PMID:20587689 PMID:15623888 PMID:14681470 |
Except where otherwise noted, Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported, Images on the database remain the property of the persons generously allowing their images to be used and are acknowledged within each record. Images should not be modified, Reproduced or disseminated without the express permission of the submitter. | biotools:pathbase, nlx_151637 | https://bio.tools/pathbase | SCR_006141 | Pathbase - European mutant mouse pathology database | 2026-08-05 10:44:26 | 11 | |||
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DARC - Database for Aligned Ribosomal Complexes Resource Report Resource Website 10+ mentions |
DARC - Database for Aligned Ribosomal Complexes (RRID:SCR_006932) | DARC | data or information resource, database, model, data analysis service, production service resource, service resource, analysis service resource | A database for aligned ribosomal complexes that provides a resource for directly comparing the structures. A collection of files deposited in the RCSB protein data bank and the Electron Microscopy Data Bank have been aligned so as to make direct comparison of the structures possible. An easy-to-use, searchable interface allows users to access and download >130 cryo-EM maps and >300 atomic models in the format of brix and pdb files, respectively. The aligned coordinate system substantially simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors. | ribosomal complex, cryo-electron microscopy, ribosomal particle, atomic model, ribosome, x-ray crystallography, structure, bio.tools |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: Electron Microscopy Data Bank at PDBe (MSD-EBI) is listed by: Debian is listed by: bio.tools has parent organization: Ludwig-Maximilians-University; Munich; Germany |
DFG SFB594; DFG SFB646; DFG WI3285/1-1 |
PMID:22009674 | biotools:darc_site, nlx_149452 | https://bio.tools/darc_site | SCR_006932 | The DARC site, Database for Aligned Ribosomal Complexes, Database for Aligned Ribosomal Complexes (DARC), DARC site | 2026-08-05 10:44:34 | 27 | |||||
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PLEXdb - Plant Expression Database Resource Report Resource Website 10+ mentions |
PLEXdb - Plant Expression Database (RRID:SCR_006963) | PLEXdb | data or information resource, data repository, portal, storage service resource, topical portal, database, data analysis service, production service resource, service resource, analysis service resource | PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data. The integrated tools of PLEXdb allow investigators to use commonalities in plant biology for a comparative approach to functional genomics through use of large-scale expression profiling data sets. | gene expression, plant, plant pathogen, genotype, phenotype, genetic, physical, pathway, plant biology, compare, functional genomics, expression profiling, expression atlas, pathogen, genome, anova, cluster, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: FuncExpression has parent organization: Iowa State University; Iowa; USA |
UniNSF DBI-0543441; NSF IOS-0922746; USDA 3625-21000-049-00D |
PMID:22084198 | biotools:plexdb, r3d100011516, nlx_149236 | https://bio.tools/plexdb, https://doi.org/10.17616/R39D13 | SCR_006963 | PLEXdb - Gene expression resources for plants and plant pathogens, Plant Expression Database | 2026-08-05 10:44:34 | 21 | |||||
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HTSeq Resource Report Resource Website 5000+ mentions |
HTSeq (RRID:SCR_005514) | HTSeq | data processing software, authoring tool, software application, standalone software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge. | python, high-throughput sequencing assay, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory |
DOI:10.1093/bioinformatics/btu638 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:htseq, OMICS_01053 | https://bio.tools/htseq | http://www-huber.embl.de/users/anders/HTSeq/, https://sources.debian.org/src/python3-htseq/ | SCR_005514 | HTSeq: Analysing high-throughput sequencing data with Python | 2026-08-05 10:44:16 | 8587 | ||||
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GeneTalk Resource Report Resource Website 10+ mentions |
GeneTalk (RRID:SCR_005231) | GeneTalk | data or information resource, data repository, narrative resource, portal, community building portal, database, storage service resource, blog, service resource | A web-based tool, knowledgebase and community for analysis and interpretation of human variant files. VCFs (Variant Call Formats) are preprocessed and annotated, you can filter them, access all databases and provide your expertise to the community by creating annotations. | sequence variant, annotation, exome sequencing, genetic variant, gene, data sharing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22826540 | The community can contribute to this resource, Free, (during beta period) | OMICS_00270, biotools:genetalk | https://bio.tools/genetalk | SCR_005231 | GeneTalk - The Professional Network and Online Tool for Geneticists | 2026-08-05 10:44:12 | 29 | |||||
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MACiE Resource Report Resource Website 1+ mentions |
MACiE (RRID:SCR_013296) | MACiE | data or information resource, database | MACiE, which stands for Mechanism, Annotation and Classification in Enzymes, is a collaborative project on enzyme reaction mechanisms. MACiE currently contains 223 fully annotated enzyme reaction mechanisms, which comprise 218 EC numbers (161 EC sub-subclasses) and 310 distinct CATH codes. It is a joint effortbetween the Mitchell Group at the Unilever Centre for Molecular Informatics part of the University of Cambridge and the Thornton Group at the European Bioinformatics Institute. | bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:macie, nif-0000-03093 | https://bio.tools/macie | SCR_013296 | The MACiE Database, Annotation and Classification in Enzymes, Mechanism | 2026-08-05 10:45:59 | 8 | |||||||
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ComiR Resource Report Resource Website 10+ mentions |
ComiR (RRID:SCR_013023) | ComiR | data analysis service, production service resource, service resource, analysis service resource | Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data. | mirna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Pittsburgh; Pennsylvania; USA |
NLM ; Fondazione RiMED |
PMID:23703208 PMID:23284279 |
Acknowledgement requested | OMICS_00395, biotools:comir | https://bio.tools/comir | SCR_013023 | Combinatorial miRNA targeting, ComiR: Combinatorial miRNA target prediction tool, ComiR - Combinatorial miRNA target prediction tool | 2026-08-05 10:45:55 | 26 | ||||
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H-InvDB Resource Report Resource Website 10+ mentions |
H-InvDB (RRID:SCR_013265) | H-InvDB, H-InvDB cDNA, H-InvDB locus | data or information resource, database | H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, and molecular evolutionary features , protein-protein interactions (PPIs) and gene families/groups. This database is produced by the Genome Information Integration Project (2005-) based upon the annotation technology established in the H-Invitational Project for annotation of human full-length cDNAs. | human gene, human genome, transcripts, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: National Institute of Advanced Industrial Science and Technology |
nif-0000-02936, biotools:h-invdb | https://bio.tools/h-invdb | SCR_013265 | H-Invitational Database, H-InvDB cDNA, H-InvDB locus, H-InvDB: Annotated Human Gene Database | 2026-08-05 10:45:53 | 24 | |||||||
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Fugu Genome Project Resource Report Resource Website 10+ mentions |
Fugu Genome Project (RRID:SCR_013014) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE,documented on August 16, 2019. Fugu genome is among the smallest vertebrate genomes and has proved to be a valuable reference genome for identifying genes and other functional elements such as regulatory elements in the human and other vertebrate genomes, and for understanding the structure and evolution of vertebrate genomes. This site presents version 4 of the Fugu genome, released in October 2004 by the International Fugu Genome Consortium. Fugu rubripes has a very compact genome, with less than 15 consisting of dispersed repetitive sequence, which makes it ideal for gene discovery. A draft sequence of the fugu genome was determined by the International Fugu Genome Consortium in 2002 using the ''whole-genome shotgun'' sequencing strategy. Fugu is the second vertebrate genome to be sequenced, the first being the human genome. This webpage presents the annotation made on the fourth assembly by the IMCB team using the Ensembl annotation pipeline. We are continuing with the gap filling work and linking of the scaffolds to obtain super-contigs. | element, evolution, fish, fugu, functional, gene, genome, human, pufferfish, regulatory, rubripes, structure, vertebrate, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Institute of Molecular and Cell Biology; Singapore; Singapore |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fugu-sg, nif-0000-20988 | https://bio.tools/fugu-sg | SCR_013014 | FGP | 2026-08-05 10:45:51 | 22 | |||||||
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PLAN2L Resource Report Resource Website |
PLAN2L (RRID:SCR_013346) | PLAN2L | data or information resource, service resource, database | A web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. The system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned. | text mining, bio-entity relation extraction, literature, information extraction, cell cycle, regulation, protein interaction, cellular location, flowering, leave, root, seed, gene, normalization, interaction, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Spanish National Cancer Research Center |
PMID:19520768 | OMICS_01192, biotools:plan2l | https://bio.tools/plan2l | SCR_013346 | PLAN2L: Plant Annotation to Literature, Plant annotation to literature | 2026-08-05 10:45:54 | 0 |
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