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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Four-dimensional Ascidian Body Atlas Resource Report Resource Website 1+ mentions |
Four-dimensional Ascidian Body Atlas (RRID:SCR_001691) | FABA | atlas, d spatial image, data or information resource | Image resource including ascidian's three-dimensional (3D) and cross-sectional images through the developmental time course. These images were reconstructed from more than 3,000 high-resolution real images collected by confocal laser scanning microscopy (CLSM) at newly defined 26 distinct developmental stages (stages 1-26) from fertilized egg to hatching larva, which were grouped into six periods named the zygote, cleavage, gastrula, neurula, tailbud, and larva periods. The data set will be helpful in standardizing developmental stages for morphology comparison as well as for providing guidelines for several functional studies of a body plan in chordate. | gene expression, genome, comparative genomics, human, microarray data, model organism, vertebrate, development, ascidian, embryonic development, embryo, video, developmental stage, 3d, slice, timelapse, egg, larva, time, confocal laser scanning microscopy | Japanese Ministry of Education Culture Sports Science and Technology MEXT ; JST-BIRD ; Japan Society for the Promotion of Science 18770207 |
PMID:17557317 | Free, Freely Available | nif-0000-02529 | http://ciona.lab.nig.ac.jp/ascidian/top.html | SCR_001691 | FABA: Four-dimensional Ascidian Body Atlas | 2026-09-12 01:01:22 | 5 | |||||
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GeneWiz browser Resource Report Resource Website 1+ mentions |
GeneWiz browser (RRID:SCR_001454) | analysis service resource, production service resource, service resource | An interactive web application for visualizing genomic data of sequenced prokaryotic chromosomes. It allows users to carry out various analyses such as mapping alignments of homologous genes to other genomes, mapping of short sequencing reads to a reference chromosome, and calculating DNA properties such as curvature or stacking energy along the chromosome. The GeneWiz browser produces an interactive graphic that enables zooming from a global scale down to single nucleotides, without changing the size of the plot. Its ability to disproportionally zoom provides optimal readability and increased functionality compared to other browsers. The tool allows the user to select the display of various genomic features, color setting and data ranges. Custom numerical data can be added to the plot allowing, for example, visualization of gene expression and regulation data. Further, standard atlases are pre-generated for all prokaryotic genomes available in GenBank, providing a fast overview of all available genomes, including recently deposited genome sequences. | genome, chromosome, alignment, homologous gene, mapping, short sequencing reads, reference chromosome | has parent organization: Technical University of Denmark; Lyngby; Denmark | PMID:21304658 | Free, Freely Available | nif-0000-08429 | SCR_001454 | 2026-09-12 01:01:22 | 6 | ||||||||
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PhenoBank Resource Report Resource Website 1+ mentions |
PhenoBank (RRID:SCR_000930) | data or information resource, database, video resource | A database that provides primary data from two high-content screens that profile the set of ~900 essential C. elegans genes (~5% of the genome) required for embryo production and/or events during the first two embryonic divisions. Phenobank houses the movies, scored defects, and phenotypic classification data for the embryo-filming and gonad morphology screens. | phenotype, data, c elegans, genome, embryo, gonad, morphology, classification | has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_73232 | SCR_000930 | 2026-09-12 01:01:21 | 1 | |||||||||
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GTEx eQTL Browser Resource Report Resource Website 100+ mentions |
GTEx eQTL Browser (RRID:SCR_001618) | data or information resource, database | Database and browser that provides a central resource to archive and display association between genetic variation and high-throughput molecular-level phenotypes. This effort originated with the NIH GTEx roadmap project: however the scope of this resource will be extended to include any available genotype/molecular phenotype datasets. | genetic variation, high-throughput, phenotype, genotype, molecular, molecule, gene, gene expression, snp, trait, expression, quantitative trait locus, expression quantitative trait locus, genome, probe, sequence, statistics, p-value, rna-seq, array, lymphoblastoid, liver, cerebellum, frontal cortex, temporal cortex, pons, gene regulation, tissue, mrna, data set | has parent organization: NCBI | NIH Common Fund 268201000029C-4-0-2 | Free, Freely available | nlx_153884 | http://www.gtexportal.org/home/ | SCR_001618 | NCBI GTEx eQTL Browser, Genotype-Tissue Expression eQTL Browser, GTEx (Genotype-Tissue Expression) eQTL Browser, NCBI GTeX eQTL Browser | 2026-09-12 01:01:22 | 499 | ||||||
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Neurospora crassa Database Resource Report Resource Website 1+ mentions |
Neurospora crassa Database (RRID:SCR_001372) | NCD | data or information resource, database | It's strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. This method is standard for microbial genome sequencing, and has been successfully applied to Drosophila. Neurospora is an ideal candidate for this approach because of the low repeat content of the genome. Neurospora crassa Database has expanded the scope of its database by including a mitochondrial annotation, incorporating information from the Neurospora compendium, and assigning NCU numbers to tRNA and rRNAs. They have improved the annotation process to predict untranslated regions and to reduce the number of spurious predictions. As a result, version 3 contains 9,826 genes, 794 fewer than version 2. During the initial phase of a WGS project they sequence both ends of the 4 kb inserts from a plasmid library prepared using randomly sheared and sized-selected DNA. The shotgun reads are assembled by recognizing overlapping regions of sequence and making use of the knowledge of the orientation and distance of the paired reads from each plasmid. Obtaining deep sequence coverage though high levels of sequence redundancy assures that the majority of the genome is represented in the initial assembly and that the consensus sequence is of high quality. Their approach toward the initial assembly was conservative, meaning they would rather fail to join sequence contigs that might overlap each other than risk making false joins between two closely related but non-overlapping genomic regions. Hence, the initial assembly contains many sequence contigs and over time these contigs will increase in size and decrease in number as they are joined together. After shotgun sequencing and assembly there was a second phase of sequencing in which additional sequence was obtained from specific regions that were missing from the original assembly or are recognized to be of low quality in the consensus. The Neurospora crassa sequencing project reflects a close collaboration between the Broad Institute and the Neurospora research community. Principal investigators include Bruce Birren and Chad Nusbaum from the Broad Institute, Matt Sachs at the Oregon Graduate Institute of Science and Technology, Chuck Staben at the University of Kentucky and Jak Kinsey at the Fungal Genetics Stock Center at the University of Kansas Medical Center. In addition, we have a larger Advisory Board made up of a number of Neurospora researchers. Sponsors: They have been funded by the National Science Foundation to sequence the N. crassa genome and make the information publicly available. | gene, annotation, compendium, contig, distance, drosophila, genome, mitochondrial, neurospora crassa, plasmid, region, rrna, sequence, trna, untranslated | Free, Freely available, | nif-0000-20965 | http://www.broadinstitute.org/annotation/genome/neurospora/Home.html | SCR_001372 | Neurospora crassa Database | 2026-09-12 01:01:22 | 4 | |||||||
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ERGO Resource Report Resource Website 50+ mentions |
ERGO (RRID:SCR_001243) | ERGO | analysis service resource, data analysis service, production service resource, service resource | A web-based genome analysis platform that integrates proprietary functional genomic data, metabolic reconstructions, expression profiling, and biochemical and microbiological data with publicly available information. Focused on microbial genomics, it provides better and faster identification of gene function across all organisms. Building upon a comprehensive genomic database integrated with a collection of microbial metabolic and non-metabolic pathways and using proprietary algorithms, it assigns functions to genes, integrates genes into pathways, and identifies previously unknown or mischaracterized genes, cryptic pathways and gene products. . * Automated and manual annotation of genes and genomes * Analysis of metabolic and non-metabolic pathways to understand organism physiology * Comparison of multiple genomes to identify shared and unique features and SNPs * Functional analysis of gene expression microarray data * Data-mining for target gene discovery * In silico metabolic engineering and strain improvement | genome analysis, genome, annotation, database, software, comparative genomics, function, gene, pathway, gene expression, microarray, FASEB list | is listed by: OMICtools | Restricted | OMICS_02097 | SCR_001243 | ERGO Genome Analysis and Discovery System, ERGO Genome Analysis & Discovery System | 2026-09-12 01:01:21 | 68 | |||||||
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COSMIC - Catalogue Of Somatic Mutations In Cancer Resource Report Resource Website 1000+ mentions |
COSMIC - Catalogue Of Somatic Mutations In Cancer (RRID:SCR_002260) | COSMIC | data or information resource, database |
Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats. Some key features of COSMIC are: * Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types. * Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines. |
cancer, mutation, somatic mutation, tumor, cancer genome, genome, gene, dna, tissue, histology, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Cancer | Wellcome Trust 077012/Z/05/Z | PMID:20952405 | Free | nif-0000-02690, biotools:cosmic, OMICS_00082 | http://www.sanger.ac.uk/perl/CGP/cosmic, https://bio.tools/cosmic | SCR_002260 | Catalogue Of Somatic Mutations In Cancer | 2026-09-12 01:01:25 | 4809 | |||
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ProTISA Resource Report Resource Website 1+ mentions |
ProTISA (RRID:SCR_002138) | ProTISA | data or information resource, database | Database of confirmed translation initiation sites (TISs) for prokaryotic genomes. The confirmed data has supporting evidence from different sources, including experiments records in the public protein database Swiss-Prot, literature, conserved domain search and sequence alignment among orthologous genes. Combing with predictions from the-state-of-the-art TIS predictor MED-Start/MED-StartPlus (in release 1.0 & 1.2) and TriTISA (since release 1.4) and annotations on potential regulatory signals, the database can serve as a refined annotation resource for the public database RefSeq. | translation initiation site, annotation, genome |
is listed by: OMICtools has parent organization: Peking University; Beijing; China |
PMID:17942412 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01871 | SCR_002138 | 2026-09-12 01:01:24 | 1 | |||||||
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Organelle Genomics Resource Report Resource Website 1+ mentions |
Organelle Genomics (RRID:SCR_002137) | OGMP | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. It investigates mitochondrial genome diversity and evolution by systematically determining the complete mitochondrial DNA (mtDNA) sequences of a phylogenetically broad selection of protists. The mtDNAs of lower fungi and choanoflagellates are being analyzed by the Fungal Mitochondrial Genome Project (FMGP), a sister project to the OGMP. | genome, mitochondrial dna, mitochondrial genome, organelle | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20928, r3d100010926 | https://doi.org/10.17616/R3TG9G | SCR_002137 | Organelle Genome Megasequencing Program | 2026-09-12 01:01:24 | 2 | |||||||
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WebGeSTer DB Resource Report Resource Website 1+ mentions |
WebGeSTer DB (RRID:SCR_002165) | WebGeSTer DB | data or information resource, database | Database of intrinsic terminators of transcription that is comprized of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. Information about structural parameters of individual terminators such as sequence, length of stem and loop, mismatches and gaps, U-trail, genomic coordinates and gene name and accession number is available in both tabular form and as a composite figure. Summary statistics for terminator profiles of whole genome can be also obtained. Raw data files for individual genomes can be downloaded (.zip files) for detailed investigations. Data is organized into different tiers such that users can fine-tune their search by entering name of the species, or taxon ID or genomes with a certain number of terminators. To visualize the occurrence of the terminators, an interactive map, with the resolution to single gene level, has been developed. | genome, terminator, transcription, plasmid, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20972211 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:webgester_db, OMICS_01862 | https://bio.tools/webgester_db | SCR_002165 | WebGesTer Database, Web Genome Scannner for Terminators Database, WebGeSTer DB - A Transcription Terminator Database | 2026-09-12 01:01:24 | 5 | |||||
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Bgee: dataBase for Gene Expression Evolution Resource Report Resource Website 50+ mentions |
Bgee: dataBase for Gene Expression Evolution (RRID:SCR_002028) | Bgee | data or information resource, database | Database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data) to anatomy and development of different species. Bgee is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of gene expression. | gene expression, scrna-seq, rna-seq, affymetrix, in situ hybridization, expressed sequence tag, cross specie, comparison, homology, anatomy, developmental stage, gene expression pattern, development, genome, function, chordate, fish, transcriptiome, embryo, adult, mirna, protein coding, prenatal, immature, post-embryonic development, alimentary system, cardiovascular system, nervous system, renal system, reproductive system, respiratory system, skeletal system, ortholog, ontology, FASEB list |
is related to: Gene Expression Omnibus is related to: NCBI Sequence Read Archive (SRA) is related to: ArrayExpress is related to: Zebrafish Information Network (ZFIN) is related to: Xenbase is related to: Mouse Genome Informatics (MGI) is related to: Berkeley Drosophila Genome Project is related to: UniGene is related to: Zebrafish Anatomical Ontology is related to: eVOC is related to: Adult Mouse Anatomy Ontology is related to: Xenopus Anatomy Ontology is related to: Drosophila anatomy and development ontologies is related to: Ensembl has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Lausanne; Lausanne; Switzerland |
Free, Freely available | nif-0000-11819, r3d100014596 | https://doi.org/10.17616/R31NJNR8 | SCR_002028 | Bgee: dataBase Gene Expression Evolution, dataBase Gene Expression Evolution | 2026-09-12 01:01:23 | 70 | ||||||
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RegPrecise Resource Report Resource Website 50+ mentions |
RegPrecise (RRID:SCR_002149) | RegPrecise | data or information resource, database | Collection of manually curated inferences of regulons in prokaryotic genomes. Database for capturing, visualization and analysis of transcription factor regulons that were reconstructed by comparative genomic approach in wide variety of prokaryotic genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | regulon, genome, transcription factor, gene, operon, transcription factor binding site, taxonomy, rna, effector, pathway, ortholog, function, FASEB list |
is listed by: OMICtools has parent organization: Lawrence Berkeley National Laboratory |
Department of Energy ; NSF DBI-0850546 |
PMID:24175918 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01869 | SCR_002149 | 2026-09-12 01:01:24 | 80 | ||||||
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Primate Orthologous Exon Database Resource Report Resource Website 1+ mentions |
Primate Orthologous Exon Database (RRID:SCR_002065) | Primate Orthologous Exon Database | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of orthologous exon regions in the genomes of human, chimpanzee, and rhesus macaque. It can be used in analysis of multi-species RNA-seq expression data, allowing for comparisons of exon-level expression across primates, as well as comparative examination of alternative splicing and transcript isoforms. | alternative splicing, transcript isoform, ortholog, exon, gene, rna-seq, primate, genome |
is listed by: OMICtools has parent organization: University of Chicago; Illinois; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01895 | SCR_002065 | 2026-09-12 01:01:23 | 1 | ||||||||
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Human Reference Genetic Material Repository Resource Report Resource Website |
Human Reference Genetic Material Repository (RRID:SCR_004693) | HuRef Repository | biomaterial supply resource, material resource | The Human Reference Genetic Material Repository makes available DNA from a single individual, J. Craig Venter, whose genome has been sequenced and assembled. The DNA samples are prepared from a lymphoblastoid cell line established at Coriell Cell Repositories from a sample of peripheral blood. The DNA samples are available in 50 microgram aliquots. The lymphoblastoid cell line is not available for distribution. The human DNA sample provided is that of J. Craig Venter whose DNA from white blood cells and sperm was sequenced using Sanger chemistry (ABI Capillary Electrophoresis Platforms 3700 and 3730xl), assembled using the Celera Assembler and was published in PLoS Biology . J. Craig Venter, born on 14 October 1946, is a Caucasian male of self-reported European-American ancestry. The data available on this sample, whose genome assembly is referred to as HuRef, includes: * Whole Genome Shotgun Sequencing data * Sequence trace set deposited by JCVI in the NCBI trace archive * Human Genome Browser displaying sequence assembly, DNA variants and gene annotations Additional data sets from this study include: * Full set of Sanger reads used for genome assembly * SNP and insertion/deletion variant on the human genome sequence coordinates (NCBI version 36) * Affymetrix 500K GeneChip data * Illumina HumanHap650Y Genotyping BeadChip data Given the amount of data publicly available the genomic content of this sample, HuRef will be useful as a reference for many genetic studies. | lymphoblastoid cell line, blood, cell culture, male, caucasian, genome, genetics, dna |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Coriell Cell Repositories has parent organization: J. Craig Venter Institute |
N/A | Public, $150 non-profit/academic, $250 commercial for 50 ug DNA | nlx_143868 | SCR_004693 | J. Craig Venter Institute Human Reference Genome (HuRef) | 2026-09-12 01:02:33 | 0 | ||||||
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Zebrafish Gene Collection Resource Report Resource Website 1+ mentions |
Zebrafish Gene Collection (RRID:SCR_007054) | ZGC | biomaterial supply resource, material resource | Part of zebrafish genome project. ZGC project to produce cDNA libraries, clones and sequences to provide complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for zebrafish. All ZGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of ZGC project in September 2008, GenBank records of ZGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which we have ZGC clones will likely change in future, users planning to order ZGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). | cdna library, clone, sequence, full-length open reading frame, cdna clone, frozen, fish, gene, genetic, genome, genomic |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: NIDDK Information Network (dkNET) is related to: Mammalian Gene Collection is related to: GenBank is related to: ATCC has parent organization: National Cancer Institute |
NIH Blueprint for Neuroscience Research | Free, Freely available | nif-0000-00567 | https://genecollections.nci.nih.gov/ZGC/ | SCR_007054 | Zebrafish Gene Collection | 2026-09-12 01:02:36 | 1 | |||||
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ZMP Resource Report Resource Website 10+ mentions |
ZMP (RRID:SCR_006161) | ZMP | biomaterial supply resource, material resource | Create knockout alleles in protein coding genes in the zebrafish genome, using a combination of whole exome enrichment and Illumina next generation sequencing, with the aim to cover them all. Each allele created is analyzed for morphological differences and published on the ZMP site. Transcript counting is performed on alleles with a morphological phenotype. Alleles generated are archived and can be requested from this site through the Zebrafish International Resource Center (ZIRC). You may register to receive updates on genes of interest, or browse a complete list, or search by Ensembl ID, gene name or human and mouse orthologue. | phenotype, genome, gene, disease model, allele, orthologue, mutant, chromosome, human orthologue, mouse orthologue, mutation, knockout, human, mouse, transcript |
is listed by: One Mind Biospecimen Bank Listing is related to: Zebrafish International Resource Center has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust Sanger Institute; Hinxton; United Kingdom ; NIH ; ZF-HEALTH |
Free and open | nlx_151662 | SCR_006161 | Zebrafish Mutation Project (ZMP), Zebrafish Mutation Project, ZMP - Zebrafish Mutation Project | 2026-09-12 01:02:35 | 25 | ||||||
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International Mouse Phenotyping Consortium (IMPC) Resource Report Resource Website 1000+ mentions |
International Mouse Phenotyping Consortium (IMPC) (RRID:SCR_006158) | IKMC, IMPC | biomaterial supply resource, material resource | Center that produces knockout mice and carries out high-throughput phenotyping of each line in order to determine function of every gene in mouse genome. These mice will be preserved in repositories and made available to scientific community representing valuable resource for basic scientific research as well as generating new models for human diseases. | phenotype, phenotyping, gene, knockout mouse, knockout, genome, function, gene function, mouse model, mutation, embryonic stem cell, genotype, disease, anatomy, procedure, image, experimental protocol, annotation, genotype-phenotype, FASEB list |
uses: LAMA is used by: NIF Data Federation is recommended by: NIDDK Information Network (dkNET) lists: VPV is listed by: One Mind Biospecimen Bank Listing is listed by: NIDDK Information Network (dkNET) is affiliated with: iMITS is related to: HARP is related to: KOMP2 is related to: Knockout Mouse Project Repository at JAX is related to: TheBehaviourForum.org is parent organization of: Impress provides: Knockout Mouse Project Repository works with: GenTaR |
NIH Office of the Director UM1 OD023222 | PMID:27626380 PMID:24652767 PMID:24197666 PMID:25127743 PMID:25343444 PMID:24642684 PMID:21677750 PMID:22968824 PMID:22940749 PMID:22991088 PMID:25992600 PMID:22566555 PMID:23519032 PMID:22211970 PMID:24194600 PMID:26147094 PMID:24634472 PMID:24932005 PMID:25093073 PMID:24046361 PMID:24033988 PMID:23315689 PMID:22926223 PMID:21185382 PMID:21737429 PMID:19933761 PMID:19689210 PMID:17905814 PMID:17218247 PMID:16933996 PMID:16254554 PMID:15908916 PMID:15340423 PMID:15340424 PMID:28650954 PMID:28650483 PMID:29026089 PMID:29348434 PMID:29352221 PMID:29396915 PMID:29626206 PMID:22566555 |
Free, Freely available | nlx_151660 | https://www.mousephenotype.org/data/documentation/data-access | SCR_006158 | KOMP, KOMP-CSD, KOMP-Regeneron, IMPC - International Mouse Phenotyping Consortium, International Mouse Phenotyping Consortium, IMPC, International Mouse Phenotyping Consortium (IMPC), EUCOMM, IKMC | 2026-09-12 01:02:35 | 2527 | ||||
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Comparative Genometrics Resource Report Resource Website |
Comparative Genometrics (RRID:SCR_012920) | data or information resource, database | The Comparative Genometrics website displays for sequenced genomes, three different genometric analyses: the DNA walk and the GC and TA skews during the initial phase. Although primarily focused on prokaryotic chromosomes, the CG website posts genometric information on paradigm plasmids, phages, viruses, and organelles. The genometric analyses are available via phylogenetic tree or alphabetical list. It also offers small genome information, for mitochondria, chloroplasts, viruses, bacteriophages, and plasmids. | genome, bacteriophages, chloroplasts, genometric analyses, mitochondria, phage, plasmids, prokaryotic chromosome, sequenced genome, viruses | has parent organization: University of Lausanne; Lausanne; Switzerland | nif-0000-02682 | SCR_012920 | Comparative Genometrics | 2026-09-12 01:02:08 | 0 | |||||||||
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Zebrafish Genome Project Resource Report Resource Website 50+ mentions |
Zebrafish Genome Project (RRID:SCR_013157) | data or information resource, database | Database of zebrafish genome. | Zebrafish, genome |
is related to: Genome Reference Consortium is related to: Zebrafish Information Network (ZFIN) has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Free, Freely available | SCR_017503, nif-0000-31931 | https://www.sanger.ac.uk/science/data/zebrafish-genome-project | SCR_013157 | Danio rerio Sequencing Project | 2026-09-12 01:02:09 | 67 | |||||||
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Tree families database Resource Report Resource Website 50+ mentions |
Tree families database (RRID:SCR_013401) | data or information resource, database | A database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families. TreeFam defines a gene family as a group of genes that evolved after the speciation of single-metazoan animals. It also tries to include outgroup genes like yeast (S. cerevisiae and S. pombe) and plant (A. thaliana) to reveal these distant members.TreeFam is also an ortholog database. Unlike other pairwise alignment based ones, TreeFam infers orthologs by means of gene trees. It fits a gene tree into the universal species tree and finds historical duplications, speciations and losses events. TreeFam uses this information to evaluate tree building, guide manual curation, and infer complex ortholog and paralog relations.The basic elements of TreeFam are gene families that can be divided into two parts: TreeFam-A and TreeFam-B families. TreeFam-B families are automatically created. They might contain errors given complex phylogenies. TreeFam-A families are manually curated from TreeFam-B ones. Family names and node names are assigned at the same time. The ultimate goal of TreeFam is to present a curated resource for all the families. phylogenetic tree, animal, vertebrate, invertebrate, gene, ortholog, paralog, evolutionary history, gene families, single-metazoan animals, outgroup genes like yeast (S. cerevisiae and S. pombe), plant (A. thaliana), historical duplications, speciations, losses, Human, Genome, comparative genomics | evolutionary history, gene, gene families, genome, animal, comparative genomics, historical duplications, human, invertebrate, losses, ortholog, outgroup genes like yeast (s. cerevisiae and s. pombe), paralog, phylogenetic tree, plant (a. thaliana), single-metazoan animals, speciations, vertebrate, FASEB list |
is related to: FlyMine has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
nif-0000-03588 | SCR_013401 | Tree families database, TreeFam | 2026-09-12 01:02:11 | 88 |
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