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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SNVrap Resource Report Resource Website 1+ mentions |
SNVrap (RRID:SCR_010512) | production service resource, data analysis service, web service, data or information resource, analysis service resource, data access protocol, service resource, software resource, data set | The web portal provides comprehensive local database of human genome variants with a user-friendly web page that provides a one-stop annotating and funtonal prediction service which is both convenient and up-to-date. A query can be accepted as either a dbSNP Id or a chromosomal location and our system will instantly provide all the annotation information in an interactive LD panel. The system can also simultaneously prioritize this variant based on additive effect mode by corresponding annotation information and evaluate the variant effect that is then displayed in a prioritization tree. Furthermore, cohort sequencing continuously produces lots of un-annotated variants such as rare variants or de novo variants, and our system can even fit this data by accepting genomic coordinates (hg19) to offer maximal annotations. Main Functions Over 40 up-to-date annotation items for human single nucleotide variations; Functional prediction for different types of variants; Dynamic LD panel for both HapMap and 1000 Genomes Project populations; Prioritization score and tree viewer based on variant functional model. | genetic variant, prioritize, genome, chromosome, functional prediction, transcription factor-binding site, mirna, mirna target site, prediction, target site, transcription factor, binding site, statistics, trait/disease-associated snp, single nucleotide polymorphism | PMID:25308971 | nlx_158733 | http://jjwanglab.org/snvrap/snvrap/snvrap/quickrap | SCR_010512 | 2026-08-03 09:34:44 | 4 | |||||||||
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TESS: Transcription Element Search System Resource Report Resource Website 100+ mentions |
TESS: Transcription Element Search System (RRID:SCR_010739) | TESS | production service resource, data analysis service, data or information resource, database, analysis service resource, service resource | TESS is a web tool for predicting transcription factor binding sites in DNA sequences. It can identify binding sites using site or consensus strings and positional weight matrices from the TRANSFAC, JASPAR, IMD, and our CBIL-GibbsMat database. You can use TESS to search a few of your own sequences or for user-defined CRMs genome-wide near genes throughout genomes of interest. Search for CRMs Genome-wide: TESS now has the ability to search whole genomes for user defined CRMs. Try a search in the AnGEL CRM Searches section of the navigation bar.. You can search for combinations of consensus site sequences and/or PWMs from TRANSFAC or JASPAR. Search DNA for Binding Sites: TESS also lets you search through your own sequence for TFBS. You can include your own site or consensus strings and/or weight matrices in the search. Use the Combined Search under ''Site Searches'' in the menu or use the box for a quick search. TESS assigns a TESS job number to all sequence search jobs. The job results are stored on our server for a period of time specified in the search submit form. During this time you may recall the search results using the form on this page. TESS can also email results to you as a tab-delimited file suitable for loading into a spreadsheet program. Query for Transcription Factor Info: TESS also has data browsing and querying capabilities to help you learn about the factors that were predicted to bind to your sequence. Use the Query TRANSFAC or Query Matrices links above or use the search interface provided from the home page. | transcription factor, dna sequence, genome, promoter, gene regulation, FASEB list | has parent organization: University of Pennsylvania; Philadelphia; USA | PMID:18428685 | nlx_97404 | http://www.pcbi.upenn.edu/tess | SCR_010739 | Transcription Element Search System | 2026-08-03 09:34:34 | 189 | ||||||
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BWA Resource Report Resource Website 1000+ mentions |
BWA (RRID:SCR_010910) | BWA | sequence analysis software, alignment software, software application, data processing software, data analysis software, image analysis software, software resource | Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp. | sequence, alignment, reference, genome, human, short, long, read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: shovill is related to: Proovread is related to: BWA-MEM2 has parent organization: SourceForge is required by: RelocaTE |
PMID:19451168 PMID:20080505 DOI:10.1093/bioinformatics/btp324 |
Free, Available for download, Freely available | SCR_015853, biotools:bwa-sw, OMICS_00654 | https://sourceforge.net/projects/bio-bwa/files/, https://bio.tools/bwa-sw, https://sources.debian.org/src/bwa/ | SCR_010910 | Burrows-Wheeler Aligner (BWA), Burrows-Wheeler Aligner | 2026-08-03 09:34:49 | 2291 | |||||
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GenomeCloud Resource Report Resource Website |
GenomeCloud (RRID:SCR_011886) | GenomeCloud | service resource, data repository, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 29, 2019. A cloud platform for next-generation sequencing analysis and storage. Services include: * g-Analysis: Automated genome analysis pipelines at your fingertips * g-Cluster: Easy-of-use and cost-effective genome research infrastructure * g-Storage: A simple way to store, share and protect data * g-Insight: Accurate analysis and interpretation of biological meaning of genome data | genome | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01219 | SCR_011886 | 2026-08-03 09:34:45 | 0 | ||||||||
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JiffyNet Resource Report Resource Website 1+ mentions |
JiffyNet (RRID:SCR_011954) | production service resource, data analysis service, software application, analysis service resource, simulation software, service resource, software resource | Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species. | protein network, protein, network, genome, sequence, pathway annotation, network visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Yonsei University; Seoul; South Korea |
National Research Foundation of Korea ; Next-Generation BioGreen 21 Program |
PMID:23685435 | Free, Freely available | OMICS_01548, biotools:jiffynet | https://bio.tools/jiffynet | SCR_011954 | 2026-08-03 09:35:01 | 1 | ||||||
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GWAS: Catalog of Published Genome-Wide Association Studies Resource Report Resource Website 500+ mentions |
GWAS: Catalog of Published Genome-Wide Association Studies (RRID:SCR_012745) | GWASC | catalog, data or information resource, database | Catalog of published genome-wide association studies. Genome-wide set of genetic variants in different individuals to see if any variant is associated with trait and disease. Database of genome-wide association study (GWAS) publications including only those attempting to assay single nucleotide polymorphisms (SNPs). Publications are organized from most to least recent date of publication. Studies are identified through weekly PubMed literature searches, daily NIH-distributed compilations of news and media reports, and occasional comparisons with an existing database of GWAS literature (HuGE Navigator). Works with HANCESTRO ancestry representation. | gene-wide association study, adult, genome, genome-wide association study, single nucleotide polymorphism, publication, literature, phenotype, trait, disease, loci, genetic variant, disorder, snp trait association |
is used by: NIF Data Federation is used by: Schizo-Pi is related to: PheWAS Catalog is related to: Psychiatric Genomics Consortium is related to: KOBAS has parent organization: National Human Genome Research Institute |
NHGRI U41 HG007823; BBSRC ; NHGRI U24 HG012542 |
PMID:19474294 | Free, Freely available | nif-0000-06666, r3d100014209 | http://www.genome.gov/gwastudies | SCR_012745 | A Catalog of Published Genome-Wide Association Studies, Catalog of Published GWAS, Catalog of published GWAS studies, NHGRI GWAS Catalog, Catalog of Published Genome-Wide Association Studies, GWAS and PGS Catalogs | 2026-08-03 09:35:05 | 859 | ||||
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KEGG Resource Report Resource Website 10000+ mentions |
KEGG (RRID:SCR_012773) | KEGG | portal, production service resource, data analysis service, web service, service resource, database, topical portal, analysis service resource, data access protocol, data or information resource, software resource | Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies. | model, pathway, functional hierarchy, module, cancer, disease, drug, drug classification, orthology, ortholog, genome, gene, protein, compound, classification, biochemical reaction, pathway, ligand, biosynthesis, pathway prediction, sequence, chemical structure, human, enzyme, database, molecular interaction, metabolism, metabolomics, cellular process, structure, drug development, reaction, cell |
is used by: NIF Data Federation is used by: Arabidopsis Reactome is used by: LIPID MAPS Proteome Database is used by: globaltest is used by: MitoMiner is used by: Database for Annotation Visualization and Integrated Discovery is used by: Biochemical Pathways Reaction Kinetics Database is used by: Ultimate Rough Aggregation of Metabolic Map is used by: GEMINI is used by: In vivo - In silico Metabolite Database is listed by: 3DVC is listed by: OMICtools is affiliated with: Kyoto Encyclopedia of Genes and Genomes Expression Database is related to: PathCase Pathways Database System is related to: ExplorEnz is related to: NCBI BioSystems Database is related to: Allen Institute Neurowiki is related to: eQuilibrator is related to: GeneTrail is related to: KegTools is related to: PRODORIC is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: METLIN is related to: Kidney and Urinary Pathway Knowledge Base is related to: DAVID is related to: ConsensusPathDB is related to: ENZYME is related to: FlyMine is related to: Babelomics is related to: SynSysNet is related to: Cotton EST Database is related to: Integrated Molecular Interaction Database is related to: SEGS is related to: INMEX is related to: BioExtract is related to: ClueGO is related to: MalaCards is related to: TrED is related to: FunTree is related to: MOPED - Model Organism Protein Expression Database is related to: ProOpDB is related to: KOBAS is related to: GeneTerm Linker is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: GeneCodis is related to: FunNet - Transcriptional Networks Analysis is related to: LegumeIP is related to: Algal Functional Annotation Tool is related to: aGEM is related to: DINIES is related to: KEGG PATHWAY Database is related to: ShinyGO is related to: KEGGREST has parent organization: Kyoto University; Kyoto; Japan has parent organization: University of Tokyo; Tokyo; Japan is parent organization of: KegTools works with: DIANA-mirPath works with: MiMeDB |
Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japan Science and Technology Agency |
PMID:22700311 PMID:22130871 PMID:22080510 PMID:19880382 PMID:19172790 PMID:18428742 PMID:18287706 PMID:18077471 PMID:16381885 PMID:16014746 PMID:14681412 PMID:12539951 PMID:11752249 PMID:10928937 PMID:10592173 PMID:9847135 |
Restricted | nlx_31015, OMICS_01583, OMICS_03010, OMICS_01582, OMICS_03974, OMICS_05434, OMICS_05360 | http://www.genome.jp/kegg/ | SCR_012773 | KEGG - Kyoto Encyclopedia of Genes and Genomes, Kyoto Encyclopedia of Genes and Genomes | 2026-08-03 09:35:05 | 75877 | ||||
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IMGT - the international ImMunoGeneTics information system Resource Report Resource Website 500+ mentions |
IMGT - the international ImMunoGeneTics information system (RRID:SCR_012780) | IMGT | portal, production service resource, data analysis service, service resource, database, topical portal, analysis service resource, data or information resource | A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools. | immunogenetics, immunoinformatics, immunoglobulin, antibody, t cell receptor, major histocompatibility complex, immunoglobulin superfamily, major histocompatibility complex superfamily, protein, immune system, sequence, genome, structure, monoclonal antibody, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: IMGT Repertoire has parent organization: Montpellier 2 University; Montpellier; France is parent organization of: IMGT/LIGM-DB is parent organization of: IMGT/GENE-DB is parent organization of: IMGT-ONTOLOGY is parent organization of: IMGT/V-QUEST is parent organization of: IMGT/HLA |
CNRS ; MESR ; Reseau National des Genopoles ; Region Languedoc-Roussillon ; European Union BIOMED1 BIOCT930038; European Union Biotechnology BIOTECH2 BIO4CT960037; European Union 5th PCRDT Quality of Life and Management of Living Resources QLG2-2000-01287; Agence Nationale de la recherche ANR BIOSYS06_135457; EU ImmunoGrid IST-028069 |
PMID:18978023 | nif-0000-03011, biotools:imgt | https://bio.tools/imgt | http://imgt.cines.fr | SCR_012780 | ImMunoGeneTics Information System, IMGT/LIGM, ImMunoGeneTics | 2026-08-03 09:35:14 | 746 | ||||
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Sequencing of Candida Albicans Resource Report Resource Website 10+ mentions |
Sequencing of Candida Albicans (RRID:SCR_013437) | topical portal, data or information resource, portal | The Stanford Genome Technology Center began a whole genome shotgun sequencing of strain SC5314 of Candida albicans. After reaching its original goal of 1.5X mean coverage of the haploid genome (16Mb) in summer, 1998, Stanford was awarded a supplemental grant to continue sequencing up to a coverage of 10X, performing as much assembly of the sequence as possible, using recognizable genes as nucleation points. Candida albicans is one of the most commonly encountered human pathogens, causing a wide variety of infections ranging from mucosal infections in generally healthy persons to life-threatening systemic infections in individuals with impaired immunity. Oral and esophogeal Candida infections are frequently seen in AIDS patients. Few classes of drugs are effective against these fungal infections, and all of them have limitations with regard to efficacy and side-effects. | stanford, genome, technology, shotgun, sequencing, strain, haploid, gene, nucleation, health, life, aids, drug, patient | has parent organization: Stanford University; Stanford; California | Burroughs Wellcome Fund ; NIDCR DE12302-02S2; NIAID RO1AI16567; NIAID RO1AI46351; NIAID NO1AI05406; NIDCR R01DE12940; NIDCR P01DE07946 |
nif-0000-30294 | SCR_013437 | Candida Albicans | 2026-08-03 09:35:15 | 21 | ||||||||
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PlasmoDB Resource Report Resource Website 1000+ mentions |
PlasmoDB (RRID:SCR_013331) | data repository, production service resource, data analysis service, web service, service resource, database, storage service resource, analysis service resource, data access protocol, data or information resource, software resource | Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene. | Functional, genomic, database, malaria, parasite, data, analysis, visualization, gene, genome, annotation, transcription, proteomics, protein, evolution, FASEB list |
uses: SynView is related to: GeneDB Pfalciparum has parent organization: Eukaryotic Pathogen Database Resources has parent organization: Pennsylvania State University has parent organization: University of Georgia; Georgia; USA |
malaria | NIAID | PMID:18957442 | nif-0000-03314, SCR_017665, r3d100011569 | SCR_013331 | PlasmoDB, Plasmodium Genomics Resource, PlasmoDB 5.5, Plasmodium genome-resource | 2026-08-03 09:35:13 | 1239 | ||||||
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PiGenome Resource Report Resource Website |
PiGenome (RRID:SCR_013394) | PiGenome | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | Database for ESTs (Expressed Sequence Tags), consensus sequences, bacterial artificial chromosome (BAC) clones, BES (BAC End Sequences). They have generated 69,545 ESTs from 6 full-length cDNA libraries (Porcine Abdominal Fat, Porcine Fat Cell, Porcine Loin Muscle, Liver and Pituitary gland). They have also identified a total of 182 BAC contigs from chromosome 6. It is very valuable resources to study porcine quantitative trait loci (QTL) mapping and genome study. Users can explore genomic alignment of various data types, including expressed sequence tags (ESTs), consensus sequences, singletons, QTL, Marker, UniGene and BAC clones by several options. To estimate the genomic location of sequence dataset, their data aligned BES (BAC End Sequences) instead of genomic sequence because Pig Genome has low-coverage sequencing data. Sus scrofa Genome Database mainly provide comparative map of four species (pig, cattle, dog and mouse) in chromosome 6. | gene expression, genome, sequence, gene, expressed sequence tag, consensus sequence, bac clone, bac end sequence, bac contig, quantitative trait loci, singleton, marker, unigene, chromosome 6, blast, transcript, bacterial artificial chromosome, snp, alignment |
is related to: Gene Ontology has parent organization: National Institute of Animal Science; Gyeonggi-do; South Korea |
National Institute of Animal Science; Gyeonggi-do; Korea ; Korean Rural Development Administration ; Biogreen21 Project 20050301034467 |
PMID:19082661 | nlx_153888 | http://pigenome.nabc.go.kr/ | SCR_013394 | Sus scrofa Genome database, Pig Genome Database, Pigenome database | 2026-08-03 09:35:12 | 0 | |||||
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ENIGMA Resource Report Resource Website 100+ mentions |
ENIGMA (RRID:SCR_013400) | software resource, data processing software, software application, data analysis software | A software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating other data types, e.g. GO annotation, protein interactions and transcription factor binding information, and by suggesting regulators that might have an effect on the expression of (some of) the genes in the module. Version : ENIGMA 1.1 used GO annotation version : Aug 29th 2007 | genome, gene, genetic software, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium is parent organization of: ENIGMA-DTI Pipeline |
PMID:18402676 | biotools:enigma, nlx_144365 | https://bio.tools/enigma | SCR_013400 | 2026-08-03 09:35:12 | 130 | ||||||||
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Genetic Association Information Network (GAIN) Resource Report Resource Website 1+ mentions |
Genetic Association Information Network (GAIN) (RRID:SCR_013703) | GAIN | consortium, organization portal, data or information resource, portal | The Genetic Association Information Network (GAIN) supports a series of Genome-Wide Association Studies (GWAS) designed to identify specific points of DNA variation associated with the occurrence of a particular common disease. Initially focusing on six major common diseases, GAIN focused on combining the results with clinical data to create a significant new resource for genetic researchers. | tool development, biomarker research, data-sharing enabler, genome, genome wide association studies, FNIH, | has parent organization: Foundation for the National Institutes of Health | Pfizer Inc ; Affymetrix Inc |
SCR_013703 | 2026-08-03 09:35:18 | 9 | |||||||||
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RAST Server Resource Report Resource Website 500+ mentions |
RAST Server (RRID:SCR_014606) | RAST | service resource, production service resource | A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes. | microbiome, seed, annotate, genome, bacteria, archaea, service, bio.tools |
is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools |
National Science Foundation 0850546; NIAID contract HHSN272200900040C |
PMID:18261238 | Free for the scientific community, Login required | biotools:theseed | https://bio.tools/theseed | SCR_014606 | Rapid Annotation using Subsystem Technology, Rapid Annotation using Subsystem Technology Server | 2026-08-03 09:35:33 | 907 | ||||
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Prokka Resource Report Resource Website 1000+ mentions |
Prokka (RRID:SCR_014732) | sequence analysis software, software application, data processing software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | annotation, prokaryote, genome, prokaryotic genome, sequence analysis software, annotation software, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btu153 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04220, biotools:prokka | https://bio.tools/prokka, https://sources.debian.org/src/prokka/, https://sources.debian.org/src/prokka/ | SCR_014732 | 2026-08-03 09:35:36 | 4876 | |||||||
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Encode Resource Report Resource Website 1000+ mentions |
Encode (RRID:SCR_015482) | organization portal, portal, consortium, data or information resource, data set | Consortium to build comprehensive parts list of functional elements in human genome. This includes elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Data from 2012-present. | genome, sequencing, protein, rna, dna, consortium |
is related to: modENCODE is related to: ENCODE is related to: 3D Genome has parent organization: Stanford University; Stanford; California has parent organization: University of California at Santa Cruz; California; USA |
NHGRI HG006992 | PMID:15499007 | Free, Freely available | SCR_015482 | ENCODE Project | 2026-08-03 09:35:59 | 1244 | |||||||
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Gene Index Project Resource Report Resource Website 100+ mentions |
Gene Index Project (RRID:SCR_002148) | TGI, DFCI TGI | portal, database, topical portal, data or information resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 19,2019.The goal of The Gene Index Project is to use the available Expressed Sequence Transcript (EST) and gene sequences, along with the reference genomes wherever available, to provide an inventory of likely genes and their variants and to annotate these with information regarding the functional roles played by these genes and their products. The promise of genome projects has been a complete catalog of genes in a wide range of organisms. While genome projects have been successful in providing reference genome sequences, the problem of finding genes and their variants in genomic sequence remains an ongoing challenge. TGI has created an inventory that contains genes and their variants together with description. In addition, this resource is attempting to use these catalogs to find links between genes and pathways in different species and to provide lists of features within completed genomes that can aid in the understanding of how gene expression is regulated. DATABASES *Eukaryotic Gene Orthologues (formerly known as TOGA - TIGR Orthologous Gene Alignment): Eukaryotic Gene Orthologues (EGO) at DFGI are generated by pair-wise comparison between the Tentative Consensus (TC) sequences that comprise the Dana Farber Gene Indices from individual organisms. The reciprocal pairs of the best match were clustered into individual groups and multiple sequence alignments were displayed for each group. *GeneChip Oncology Database (GCOD):Cancer gene expression database is a collection of publicly available microarray expression data on Affymetrix GeneChip Arrays related to human cancers. Currently only datasets with available raw data (Affymetrix .CEL files) are processed. All processed datasets were subjected to extensive manual curation, uniform processing and consistent quality control. You can browse the experiments in our collection, perform statistical analysis, and download processed data; or to search gene expression profiles using Entrez gene symbol, Unigene ID, or Affymetrix probeset ID. *Gene Indices: As of July 1, 2008, there are 111 publicly available gene indices. They are separated into 4 categories for better organization and easier access. Animal: 41, Plant: 45, Protist: 15, Fungal: 10 *Genomic Maps: Human, mouse, rat, chicken, drosophila melanogaster, zebrafish, mosquito, caenorhabditis elegans, Arabidopsis thaliana, rice, yeast, fission yeast Dana-Farber Cancer Institute (DFCI) Gene Indices Software Tools: *TGI Clustering tools (TGICL): a software system for fast clustering of large EST datasets. *GICL: this package contains the scripts and all the necessary pre-compiled binaries for 32bit Linux systems. *clview: an assembly file viewer. *SeqClean:a script for automated trimming and validation of ESTs or other DNA sequences by screening for various contaminants, low quality and low-complexity sequences. *cdbfasta/cdbyank: fast indexing/retrieval of fasta records from flat file databases. *DAS/XML Genomic Viewer The Genomic viewer borrows modules from http://www.biodas.org (lstein (at) cshl.org) & http://webreference.com. | functional, gene, genome, index, organism, pathway, product, role, sequence, species, transcript, variant, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Dana-Farber Cancer Institute |
DOE DBI-0552416 | PMID:7566098 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tigr_gene_indices, nif-0000-20942 | https://bio.tools/tigr_gene_indices | SCR_002148 | DFCI Gene Index Project, Gene Index Project, DFCI | 2026-08-03 09:31:46 | 129 | ||||
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CYGD - Comprehensive Yeast Genome Database Resource Report Resource Website 10+ mentions |
CYGD - Comprehensive Yeast Genome Database (RRID:SCR_002289) | CYGD | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition, the data of various projects on related yeasts are used for comparative analysis. | saccharomyces cerevisiae, yeast, yeast genome, genome | is related to: FunSpec | Federal Ministry of Education Science Research and Technology ; European Union ; Government of the Brussels Region - Belgium ; DFG |
PMID:15608217 | nif-0000-02713 | SCR_002289 | MIPS Saccharomyces cerevisiae genome database, MIPS Comprehensive Yeast Genome Database, Comprehensive Yeast Genome Database | 2026-08-03 09:31:45 | 14 | ||||||
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Neisseria meningitidis MC58 Genome Page Resource Report Resource Website 1+ mentions |
Neisseria meningitidis MC58 Genome Page (RRID:SCR_002200) | topical portal, data or information resource, database, portal | Portal contains detailed information for Neisseria meningitidis MC58. Information include DNA molecule summary, primary annotation summary, and taxonomy. It is a tool that allows the researcher to access all of the bacterial genome sequences completed to date. Users may access information on all of the bacterial genomes or any subset of them. Information in the website about its DNA molecule includes: total number of DNA molecules, total size of all DNA molecules, number of primary annotation coding bases, and number of G + C bases. Its primary annotation summary include: total genes, protein coding genes, tRNA genes, and rRNA genes. Sponsors: The CMR was previously funded by two grants, one from the U.S. Department of Energy (DOE) and one from the National Science Foundation (NSF). It is currently partially funded by a Microbial Sequence Center (MSC) grant from the National Institute of Allergy and Infectious Diseases (NIAID) | gene, annotation, bacterial, coding, dna, genome, mc58, molecule, neisseria meningitidis, protein, rrna, taxonomy, trna | Free, Freely available | nif-0000-20964 | http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?database=gnm | SCR_002200 | NMMGP | 2026-08-03 09:31:42 | 1 | ||||||||
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CTCFBSDB Resource Report Resource Website 50+ mentions |
CTCFBSDB (RRID:SCR_002279) | CTCFBSDB, CTCFBSDB 2.0 | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource |
A comprehensive collection of experimentally determined and computationally predicted CCCTC-binding factor (CTCF) binding sites (CTCFBS) from the literature. The database is designed to facilitate the studies on insulators and their roles in demarcating functional genomic domains. The CTCFBS Prediction Tool allows users to scan sequences for the single best match to CTCF position weight matrices. Currently (March 2014), the database contains almost 15 million experimentally determined CTCF binding sites across several species. CTCF binding sites were collected from published papers containing CTCF binding sites identified using ChIPSeq or similar methods, data from the ENCODE project, and a set of approximately 100 manually curated binding sites identified by low-throughput experiments. Users can browse insulator sequence features, function annotations, genomic contexts including histone methylation profiles, flanking gene expression patterns and orthologous regions in other mammalian genomes. Users can also retrieve data by text search, sequence search and genomic range search. |
cctc-binding factor, ctcf, ctcf binding site, insulator, genomic insulator, genome, binding site, FASEB list |
is listed by: OMICtools has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PMID:23193294 PMID:17981843 |
nif-0000-02703, OMICS_00530 | http://insulatordb.utmem.edu/ | SCR_002279 | CTCFBSDB: a CTCF binding site database for characterization of vertebrate genomic insulators, CTCFBSDB 2.0: A database for CTCF binding sites and genome organization | 2026-08-03 09:31:44 | 63 |
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