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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ViralZone Resource Report Resource Website 100+ mentions |
ViralZone (RRID:SCR_006563) | ViralZone | data or information resource, database | ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries. ViralZone project is handled by the virus program of SwissProt group. Proteins popups were developed in collaboration with Prof. Christian von Mering and Andrea Franceschini, Bioinformatics Group , Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland, funded in part by the SIB Swiss Institute of bioinformatics. All pictures in ViralZone are copyright of the SIB Swiss Institute of Bioinformatics. | dna virus, rna virus, virus, dna, rna, genomic, proteomic, sequence, reference strain, image, virion, retro-transcribing virus, genome, bibliographic, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics |
Swiss Institute of Bioinformatics | PMID:20947564 | biotools:viralzone, r3d100013314, nlx_144372 | https://bio.tools/viralzone https://doi.org/10.17616/R31NJMRM |
http://www.expasy.org/viralzone/ | SCR_006563 | Viral Zone | 2026-02-14 02:06:34 | 128 | ||||
|
neuroelectro Resource Report Resource Website 10+ mentions |
neuroelectro (RRID:SCR_006274) | NeuroElectro | data or information resource, database | A database of elecrophysiological properties text-mined from the biomedical literature as a function of neuron type. Specifically, NeuroElectro seeks to extract information about the electrophysiological properties (e.g. resting membrane potentials and membrane time constants) of diverse neuron types from the existing literature and place it into a centralized database. There are 252 neurons currently available, with the naming convention established in NeuroLex. | electrophysiology, text mining, cellular neurophysiology, neuron, neuron electrophysiology, bio.tools |
is used by: NIF Data Federation is listed by: Debian is listed by: bio.tools is related to: NeuroLex has parent organization: Carnegie Mellon University; Pennsylvania; USA |
Open unspecified license | nlx_151885, BioTools:neuroelectro, biotools:neuroelectro, r3d100011798 | https://bio.tools/neuroelectro https://bio.tools/neuroelectro https://bio.tools/neuroelectro https://doi.org/10.17616/R3BP7F |
SCR_006274 | Neuro Electro, NeuroElectro: organizing information on cellular neurophysiology | 2026-02-14 02:05:55 | 27 | ||||||
|
Scansite Resource Report Resource Website 100+ mentions |
Scansite (RRID:SCR_007026) | data or information resource, database | Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains. The Motifscanner program utilizes an entropy approach that assesses the probability of a site matching the motif using the selectivity values and sums the logs of the probability values for each amino acid in the candidate sequence. The program then indicates the percentile ranking of the candidate motif in respect to all potential motifs in proteins of a protein database. When available, percentile scores of some confirmed phosphorylation sites for the kinase of interests or confirmed binding sites of the domain of interest are provided for comparison with the scores of the candidate motifs. | binding, kinase, phosphorylate, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
biotools:scansite, nif-0000-20914 | https://bio.tools/scansite | SCR_007026 | Scansite | 2026-02-14 02:06:35 | 297 | ||||||||
|
HIstome: The Histone Infobase Resource Report Resource Website 1+ mentions |
HIstome: The Histone Infobase (RRID:SCR_006972) | HIstome | data or information resource, database | Database of human histone variants, sites of their post-translational modifications and various histone modifying enzymes. The database covers 5 types of histones, 8 types of their post-translational modifications and 13 classes of modifying enzymes. Many data fields are hyperlinked to other databases (e.g. UnprotKB/Swiss-Prot, HGNC, OMIM, Unigene etc.). Additionally, this database also provides sequences of promoter regions (-700 TSS +300) for all gene entries. These sequences were extracted from the UCSC genome browser. Sites of post-translational modifications of histones were manually searched from PubMed listed literature. Current version contains information for about ~50 histone proteins and ~150 histone modifying enzymes. HIstome is a combined effort of researchers from two institutions, Advanced Center for Treatment, Research and Education in Cancer (ACTREC), Navi Mumbai and Center of Excellence in Epigenetics (CoEE), Indian Institute of Science Education and Research (IISER), Pune. | histone, protein, enzyme, modifying enzyme, post-translational modification, variant, promoter region, gene, epigenetic regulation, india, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools has parent organization: ACTREC - Advanced Centre for Treatment Research and Education in Cancer |
Cancer | ACTREuropean Union - Advanced Centre for Treatment Research and Education in Cancer ; Government of India |
PMID:22140112 | Free, Public, Acknowledgement requested | biotools:histome, r3d100010977, nlx_151419 | http://www.actrec.gov.in/histome/ https://bio.tools/histome https://doi.org/10.17616/R3RD0R |
http://www.histome.net/ | SCR_006972 | 2026-02-14 02:05:57 | 1 | |||
|
Midbody, Centrosome and Kinetochore Resource Report Resource Website 10+ mentions |
Midbody, Centrosome and Kinetochore (RRID:SCR_007052) | MiCroKit | data or information resource, database | MiCroKit database is the first integrative resource to pin point most of identified components and related scientific information of midbody, centrosome and kinetochore. In this work, we have collected all proteins identified to be localized on kinetochore, centrosome, and/or midbody from two fungi (S. cerevisiae and S. pombe) and five animals, including C. elegans, D. melanogaster, X. laevis, M. musculus and H. sapiens. From the related literature of PubMed, numerous proteins have been manually curated to be localized on at least one of the sub-cellular localizations of kinetochore, centrosome and midbody. And to promise the quality of data, based on the rationale of Seeing is believing (Bloom K et al., 2005), these proteins have been unambiguously observed under fluorescent microscope as directly supportive evidences. Then an integrated and searchable database MiCroKit - Midbody, Centrosome and Kinetochore has been established. The version 1.0 of MiCroKit database was set up on Nov. 2nd, 2005, containing 1,065 unique proteins. The MiCroKit version 2.0 was released on Jun. 5th, 2006, with 1,120 entries. Currently, the MiCroKit 3.0 database was updated on July 9, 2009, containing 1,489 unique protein entries. The online service of MiCroKit 3.0 was implemented in PHP + MySQL + JavaScript. And the local packages of MiCroKit 3.0 were developed in JAVA 1.5 (J2SE). The database will be updated routinely as new microkit proteins are reported. | bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Huazhong University of Science and Technology; Wuhan; China |
PMID:19783819 | r3d100010550, nif-0000-03126, biotools:microkit | https://bio.tools/microkit https://doi.org/10.17616/R32P6K |
http://bioinformatics.lcd-ustc.org/microkit/ | SCR_007052 | MiCroKit - An Integrated Database of Midbody Centrosome and Kinetochore, MiCroKit - An Integrated Database of Midbody Centrosome Kinetochore, MiCroKit database, MiCroKit - Midbody Centrosome and Kinetochore, MiCroKit - Midbody Centrosome Kinetochore | 2026-02-14 02:06:02 | 11 | |||||
|
BioCarta Pathways Resource Report Resource Website 1000+ mentions |
BioCarta Pathways (RRID:SCR_006917) | data or information resource, database | BioCarta Pathways allows users to observe how genes interact in dynamic graphical models. Online maps available within this resource depict molecular relationships from areas of active research. In an open source approach, this community-fed forum constantly integrates emerging proteomic information from the scientific community. It also catalogs and summarizes important resources providing information for over 120,000 genes from multiple species. Find both classical pathways as well as current suggestions for new pathways. | graphical model, molecular interaction, molecular relationship, pathway, proteomics, bio.tools, FASEB list |
is used by: Database for Annotation Visualization and Integrated Discovery is listed by: bio.tools is listed by: Debian is related to: Pathway Interaction Database is related to: DAVID is related to: ConsensusPathDB is related to: Babelomics is related to: ClueGO is related to: KOBAS is related to: hiPathDB - human integrated Pathway DB with facile visualization |
nif-0000-02604, biotools:biocarta | https://bio.tools/biocarta | http://www.biocarta.com/genes/allPathways.asp | SCR_006917 | BioCarta Pathways | 2026-02-14 02:06:27 | 1118 | |||||||
|
IMGT/LIGM-DB Resource Report Resource Website 10+ mentions |
IMGT/LIGM-DB (RRID:SCR_006931) | IMGT LIGM, IMGT/LIGM | data or information resource, database | IMGT/LIGM-DB is a comprehensive database of immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and other vertebrate species (270). IMGT/LIGM-DB includes all germline (non-rearranged) and rearranged IG and TR genomic DNA (gDNA) and complementary DNA (cDNA) sequences published in generalist databases. IMGT/LIGM-DB allows searches from the Web interface according to biological and immunogenetic criteria through five distinct modules depending on the user interest. Users can search the catalogue by accession number, mnemonic, definition, creation date, length, or annotation level. They also have the option to search through taxonomic classification, keywords, and annotated labels. For a given entry, nine types of display are available including the IMGT flat file, the translation of the coding regions and the analysis by the IMGT/V-QUEST tool (see parent org. below). IMGT/LIGM-DB distributes expertly annotated sequences. The annotations hugely enhance the quality and the accuracy of the distributed detailed information. They include the sequence identification, the gene and allele classification, the constitutive and specific motif description, the codon and amino acid numbering, and the sequence obtaining information, according to the main concepts of IMGT-ONTOLOGY. They represent the main source of IG and TR gene and allele knowledge stored in IMGT/GENE-DB and in the IMGT reference directory., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | nucleotide sequence, gold standard or authority, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: IMGT - the international ImMunoGeneTics information system |
PMID:16381979 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:IMGt_LIGM-Db, nif-0000-03015, r3d100012534 | https://bio.tools/IMGT_LIGM-DB https://doi.org/10.17616/R3VV2X |
http://imgt.cines.fr, http://imgt.cines.fr/cgi-bin/IMGTlect.jv | SCR_006931 | IMGT LIGM, IMGT/LIGM, ImMunoGeneTics/Laboratoire d''ImmunoGenetique Moleculaire-Database | 2026-02-14 02:06:27 | 16 | ||||
|
Database of Arabidopsis Transcription Factors Resource Report Resource Website 10+ mentions |
Database of Arabidopsis Transcription Factors (RRID:SCR_007101) | DATF | data or information resource, database | Database that collects all arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families. It uses not only locus (gene), but also gene model (transcript, protein) and the detail information is for each gene model not for locus. It adds multiple alignment of the DNA-binding domain of each family, Neighbor-Joining phylogenetic tree of each family, the GO annotation, homolog with the Database of Rice Transcription Factors (DRTF). It also keeps old information items such as the unique cloned and sequenced information of about 1200 transcription factors, protein domains, 3D structure information with BLAST hits against PDB, predicted Nuclear Location Signals, UniGene information, as well as links to literature reference. | gene, alignment, arabidopsis, binding, clone, dna, domain, locus, phylogenetic tree, transcription, chromosome, transcription factor, blast, family, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Peking University; Beijing; China |
State Key Laboratory of Protein and Plant Gene Research ; National Natural Science Foundation of China 31470330; China 863 Programs 2006AA02Z334; China Postdoctoral Science Foundation Grant 2014M560017 |
PMID:15731212 | Free | nif-0000-21112, OMICS_00551, biotools:datf | https://bio.tools/datf | SCR_007101 | 2026-02-14 02:06:35 | 36 | |||||
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Polygenic Pathways Resource Report Resource Website 1+ mentions |
Polygenic Pathways (RRID:SCR_006962) | data or information resource, database | Database of disease genes and risk factors and of host pathogen/interactomes. Lists genes, pathways and environmental risk factors positively associated with diseases and conditions such as Alzheimer's disease, schizophrenia, multiple sclerosis, childhood obesity, anorexia nervosa, HIV-1/AIDS, and helicobacter pylori. Details of polymorphisms as well as negative/positive association data can be found via Useful links. Throughout the site are links to Entrez Gene and Pubmed. | genetic disease, risk factor, host pathogen, interactome, polygenic pathway, bio.tools |
is listed by: bio.tools is listed by: Debian is parent organization of: Polygenic Pathways Jobs is parent organization of: PolygenicBlog |
Alzheimer's disease, Schizophrenia, Bipolar disorder, depression, Parkinson's disease, Huntington's disease, Multiple sclerosis, Cystic fibrosis, Childhood obesity, Chronic fatigue syndrome, Autism, Anorexia nervosa, Attention deficit hyperactivity disorder, HIV-1/AIDS | Google ; Amazon |
Free, Freely available | nif-0000-00514, biotools:polygenicpathways, SCR_015716 | https://bio.tools/polygenicpathways | SCR_006962 | PolygenicPathways, Polygenic Signaling Pathways | 2026-02-14 02:06:35 | 4 | |||||
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HaploReg Resource Report Resource Website 1000+ mentions |
HaploReg (RRID:SCR_006796) | HaploReg | data or information resource, database | HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using linkage disequilibrium (LD) information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation. | chromatin state, conservation, regulatory motif, alteration, variant, chromatin, motif, annotation, genome, variation, genome-wide association study, refsnp, refseq gene, snp, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Broad Institute |
NHGRI R01-HG004037; NHGRI RC1-HG005334; NSF 0644282 |
PMID:22064851 | biotools:HaploReg, nlx_151407 | http://compbio.mit.edu/HaploReg https://bio.tools/HaploReg |
SCR_006796 | 2026-02-14 02:06:27 | 1004 | ||||||
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CATdb: a Complete Arabidopsis Transcriptome database Resource Report Resource Website 10+ mentions |
CATdb: a Complete Arabidopsis Transcriptome database (RRID:SCR_007582) | data or information resource, database | CATdb collects together all the information on transcriptome experiments done at URGV with CATMA micro arrays. All data in CATdb come from the URGV micro array platforms. Common procedures are used including any steps from the experiment design to the statistical analyses. Directed through a WEB interface, biologists enter the standard description of each experimental step (extraction, labelling, hybridization and scanning). Then, normalization and statistical analyses are done following a set of selected methods depending on the experimental design and array types. | catma, microarray, transcriptome, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Evry-Val d'Essonne; Ile-de-France; France |
nif-0000-02639, biotools:catdb | https://bio.tools/catdb | SCR_007582 | CATdb | 2026-02-14 02:06:29 | 40 | ||||||||
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Allele Frequencies in Worldwide Populations Resource Report Resource Website 100+ mentions |
Allele Frequencies in Worldwide Populations (RRID:SCR_007259) | data or information resource, database | The main purpose of the allelefrequencies.net website is to provide one central source, freely available to all. For the storage of allele frequencies from different polymorphic areas in the HUMAN genome. Users can contribute the results of their work into one common database, and can perform database searches on information already available. They have currently collected data in allele, haplotype and genotype format. The success of this website will depend on you to contribute your data. Sponsors: This resource is supported Royal Liverpool University. Keywords: Allele, Polymorphic, Genome, Database, Data, Haplotype, Genotype, | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Royal Liverpool University; Liverpool; United Kingdom |
r3d100011904, biotools:allele_frequency_net, nif-0000-30079 | https://bio.tools/allele_frequency_net https://doi.org/10.17616/R3F063 |
SCR_007259 | Allele Frequencies | 2026-02-14 02:06:03 | 411 | ||||||||
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Full-Length cDNA Database Resource Report Resource Website 1+ mentions |
Full-Length cDNA Database (RRID:SCR_007666) | data or information resource, database | Full-Length cDNA Database is a resource for cDNA libraries of arhtropods and parasites. The arthropod species covered are Anopheles stephensi, Glossina morsitans (Tsetse fly), and Dermatophagoides farinae (House dust mite), while the parasitic species included are Plasmodium falciparum (Malaria), Toxoplasma gondii, Cryptosporidium parvum, Babesia bovis (Babesia), and Echinococcus multilocularis. A specialized database of each species is available as a link from the home page. This database has been constructed and maintained since 2001 by a Grant-in-Aid for Publication of Scientific Research Results from the Japan Society for the Promotion of Science. Anopheles stephensi, Glossina morsitans, Tsetse fly, Dermatophagoides farinae, House dust mite, Plasmodium falciparum, Malaria, Toxoplasma gondii, Cryptosporidium parvum, Babesia bovis, Babesia, Echinococcus multilocularis, cDNA, cDNA library, arthropod genome, parasite genome | echinococcus multilocularis, anopheles stephensi, arthropod genome, babesia, babesia bovis, cdna, cdna library, cryptosporidium parvum, dermatophagoides farinae, glossina morsitans, house dust mite, malaria, parasite genome, plasmodium falciparum, toxoplasma gondii, tsetse fly, bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:full-parasites, nif-0000-02856 | https://bio.tools/full-parasites | SCR_007666 | Full-Length cDNA Database | 2026-02-14 02:06:37 | 6 | ||||||||
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miROrtho: the catalogue of animal microRNA genes Resource Report Resource Website 1+ mentions |
miROrtho: the catalogue of animal microRNA genes (RRID:SCR_007797) | data or information resource, database | It contains predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline. The current release of miROrtho covers 46 animal genomes. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Geneva; Geneva; Switzerland |
nif-0000-03139, biotools:mirortho | https://bio.tools/mirortho | SCR_007797 | miROrtho | 2026-02-14 02:06:08 | 4 | ||||||||
|
Noncoding RNA database Resource Report Resource Website 10+ mentions |
Noncoding RNA database (RRID:SCR_007815) | ncRNA | data or information resource, database | It is intended to provide information on the sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell. Currently, the database includes over 30,000 individual sequences from 99 species of Bacteria, Archaea and Eukaryota. The primary source of sequences included in the database was the GenBank. Additional annotation information for mouse and human ncRNAs was derived from FANTOM3 database and H-inviational Integrated Database of Annotated Human Genes version 3.4, respectively. Genome mapping information was derived from tha data available at the UCSC Genome Browser site. The sequences and annotations of small cytoplasmic RNAs from bacteria, for which annotation is lacking in the genome sequences, were derived from the Rfam database. The microRNAs or snoRNAs which were available in previous editions, as well as other housekeeping (infrastructural) RNAs (e.g. rRNA, tRNA, snRNA, SRP RNA) are not included in our database to avoid redundancy with more specialized databases which emerged in recent years. | bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-03183, biotools:ncrna | https://bio.tools/ncrna | SCR_007815 | Noncoding RNA database | 2026-02-14 02:06:31 | 13 | |||||||
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IMG Resource Report Resource Website 500+ mentions |
IMG (RRID:SCR_007733) | IMG | data or information resource, database | Datasets and tools for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context. Plasmids that are not part of a specific microbial genome sequencing project and phage genomes are also included in order to increase its genomic context for comparative analysis. The user interface (see User Interface Map) allows navigating the microbial genome data space along its three key dimensions (genes, genomes, and functions), and groups together the main comparative analysis tools. Microbial genome data analysis in IMG usually starts with the definition of an analysis context in terms of selected genomes, functional annotations, and/or genes, followed by the individual or comparative analysis of genomes, functional annotations, or genes. | genome, microorganism, annotation, bio.tools, FASEB list |
is listed by: 3DVC is listed by: bio.tools is listed by: Debian has parent organization: DOE Joint Genome Institute |
nif-0000-03009, biotools:img | https://bio.tools/img | SCR_007733 | Integrated Microbial Genomes | 2026-02-14 02:06:02 | 652 | |||||||
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MetaCyc Resource Report Resource Website 1000+ mentions |
MetaCyc (RRID:SCR_007778) | MetaCyc | data or information resource, database | MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1,200 pathways from more than 1,600 different organisms, and is curated from the scientific experimental literature. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated compounds, enzymes, and genes. | bio.tools, FASEB list |
uses: Pathway Tools is listed by: BioCyc is listed by: bio.tools is listed by: Debian is related to: BioCyc is related to: ENZYME is related to: NCBI BioSystems Database is related to: Algal Functional Annotation Tool is related to: Pathway Tools has parent organization: Stanford Research Institute International works with: MiMeDB |
r3d100011294, nif-0000-03114, biotools:metacyc | https://bio.tools/metacyc https://doi.org/10.17616/R32K7X |
SCR_007778 | 2026-02-14 02:06:31 | 1761 | ||||||||
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MEROPS Resource Report Resource Website 500+ mentions |
MEROPS (RRID:SCR_007777) | MEROPS, MEROPS fam | data or information resource, database | An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. The MEROPS database uses an hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of statistically significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan. There is a Summary page for each family and clan, and these have indexes. Each of the Summary pages offers links to supplementary pages. About 3000 individual peptidases and inhibitors are included in the database, and there is a Summary page describing each one. You can navigate to this by any of several routes. There are indexes of Name, MEROPS Identifier and source Organism on the menu bar. Each Summary page describes the classification and nomenclature of the peptidase or inhibitor, and provides links to supplementary pages showing sequence identifiers, the structure if known, literature references and more. | peptidase, protease, proteinase, proteolytic enzyme, protein, inhibitor, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: TopFIND has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust WT077044/Z/05/Z | PMID:19892822 | biotools:merops, r3d100012783, nif-0000-03112 | https://bio.tools/merops https://doi.org/10.17616/R33225 https://doi.org/10.17616/R33225 |
SCR_007777 | MEROPS- the Peptidase Database, MEROPS - the Peptidase Database, MEROPS database, MEROPS fam | 2026-02-14 02:06:03 | 736 | |||||
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LOCATE: subcellular localization database Resource Report Resource Website 50+ mentions |
LOCATE: subcellular localization database (RRID:SCR_007763) | data or information resource, database | LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set. The membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing peer-reviewed publications. | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Queensland; Brisbane; Australia |
nif-0000-03086, biotools:locate | https://bio.tools/locate | SCR_007763 | LOCATE | 2026-02-14 02:06:38 | 66 | ||||||||
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PhyloPat Resource Report Resource Website 1+ mentions |
PhyloPat (RRID:SCR_007851) | data or information resource, database | A database of phylogenetic patterns of evolution between 46 different species. PhyloPat uses the latest release of EnsMart (release 52), and their one-to-one, one-to-many and many-to-many orthologies. First, we stored all of the Ensembl IDs within the 46 species, and the orthologies between them. Second, we determined the evolutionary order of the studied species using the NCBI Taxonomy database. The phylogenetic tree of these species can be viewed here. Third, we used this phylogenetic tree as a starting point for building our phylogenetic lineages. For each gene in the first species (S. cerevisiae), we looked for orthologs in the other species. All orthologs were added to the phylogenetic lineage, and in the next round were checked for orthologs themselves, until no more orthologies were found for any of the genes. This process was repeated for all genes in all species that were not connected to any phylogenetic lineage yet. The complete phylogenetic lineage determination generated 329,998 phylogenetic lineages, consisting of 973,821 genes. These lineages can be queried here by phylogenetic patterns, MySQL regular expressions or simply a list of Ensembl/EMBL/EntrezGene/HGNC IDs. Output can be given in HTML, Excel or plain text format. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Radboud University; Nijmegen; The Netherlands |
nif-0000-03282, biotools:phylopat | https://bio.tools/phylopat | SCR_007851 | PhyloPat | 2026-02-14 02:06:04 | 2 |
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