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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GEUVADIS Resource Report Resource Website 1+ mentions |
GEUVADIS (RRID:SCR_000684) | GEUVADIS | data or information resource, organization portal, consortium, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. A European Medical Sequencing Consortium committed to gaining insights into the human genome and its role in health and medicine by sharing data, experience and expertise in high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genetic, variation, health, disease, medical, sequencing, high-throughput sequencing, human genome, genome, genomics, personalized medicine, genomic medicine | is listed by: OMICtools | European Union ; FP7 ; HEALTH |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01779, SCR_013706 | SCR_000684 | Genetic European Variation in Health and Disease - A European Medical Sequencing Consortium, GEUVADIS Consortium, Genetic European Variation in Health and Disease | 2026-07-28 09:40:05 | 1 | ||||||
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EUCOMMTOOLS Resource Report Resource Website 1+ mentions |
EUCOMMTOOLS (RRID:SCR_000676) | EUCOMMTOOLS | material service resource, service resource, production service resource, biomaterial manufacture | Functional Annotation of the Mouse Genome, it will complete the International Knockout Mouse Consortium (IKMC) resource of mutations for all protein coding genes. Furthermore, it will maximize the utility of the conditional IKMC resource by generating up to 250 different, mostly inducible Cre driver mouse lines. In addition, EUCOMMTOOLS will develop novel tools to enhance the versatility of the IKMC resource. EUCOMMTOOLS vectors, mutant ES cells and mutant mice are distributed worldwide: EUCOMMTOOLS mutant ES cells and vectors can be obtained from the European Mouse Mutant Cell Repository (EuMMCR). EUCOMMTOOLS mutant mice are archived and distributed by the European Mouse Mutant Archive (EMMA). Knockout-first Mutant Alleles: EUCOMMTOOLS will create 3500 C57Bl/6 conditional mutant alleles for single-exon (or otherwise previously conditionally untargeted) protein-coding mouse genes. These alleles will be made predominantly by introducing an "artificial intron", containing a standard EUCOMM promoter-driven targeting cassette, into the coding sequence of the single-exon gene. Cre Resources: EUCOMMTOOLS will engineer 500 new Cre C57Bl/6 ES cell lines by Cre knock-ins into genes with useful expression patterns. The resource will be made with inducible forms of Cre recombinase such as CreERT2. Up to 250 lines of Cre driver mice on a pure C57Bl/6N background will be generated and the Cre expression patterns documented and annotated in day P14 and P56. These mice will form a matched Cre driver resource for C57Bl/6N mice produced from conditional IKMC resources. Research, Technology and Complementary Reagents: EUCOMMTOOLS will develop novel technologies to add value, depth and flexibility to existing IKMC ES cell and mouse resources. Key areas include: * Development of novel recombinase based regulatory switches * Exploration of zinc-finger nuclease stimulated homologous recombination strategies in fertilized oocytes * Development and validation of complementary modular vector reagents which enable the construction of new useful knock-in alleles such as fluorescent and other reporters, site specific recombinases, and mutant cDNAs. These novel alleles can be constructed either by re-utilizing existing IKMC modular vector resources or directly modifying existing targeted IKMC ES cell lines by RMCE. | genome, annotation, function, mutation, protein coding gene, vector, mutant embryonic stem cell, mutant mouse strain, cre driver, cre, recombinase, c57bl/6, allele, embryonic stem cell line, c57bl/6n, knock-in |
uses: EuMMCR uses: European Mouse Mutant Archive is related to: Recombinase (cre) Activity has parent organization: International Knockout Mouse Consortium |
European Union ; FP7 ; THEME Health |
nlx_152804 | SCR_000676 | EUCOMM - Tools for Functional Annotation of the Mouse Genome, EUCOMM: Tools for Functional Annotation of the Mouse Genome | 2026-07-28 09:40:02 | 1 | |||||||
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MEGA Resource Report Resource Website 1000+ mentions |
MEGA (RRID:SCR_000667) | MEGA, MEGA6, MEGA4, MEGA 4, MEGA 11 | software application, data analysis software, sequence analysis software, software resource, data processing software, software toolkit | Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny. | comparative, analysis, DNA, protein, sequence, molecular, evolution, pattern, gene, genome, evolution, FASEB list | has parent organization: Pennsylvania State University | Japan Society for the Promotion of Science ; NHGRI HG006039; NHGRI HG002096; Burroughs-Wellcome Fund ; NIGMS R01GM126567; NSF ABI 1661218; NIGMS R35GM139504 |
DOI:10.1093/molbev/msab120 PMID:24132122 PMID:31904846 PMID:22923298 PMID:21546353 PMID:17488738 PMID:15260895 PMID:11751241 PMID:8019868 |
Free, Available for download, Freely available | SCR_023017, nlx_156838 | https://www.megasoftware.net/mega4/ | SCR_000667 | MEGA11, Molecular Evolutionary Genetics Analysis, Molecular Evolutionary Genetics Analysis 6, Molecular Evolutionary Genetics Analysis 4 | 2026-07-28 09:40:02 | 2763 | ||||
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Golden Helix GenomeBrowse Resource Report Resource Website 1+ mentions |
Golden Helix GenomeBrowse (RRID:SCR_001213) | GenomeBrowse | software application, software resource, data processing software, data visualization software, commercial organization | Software tool that delivers visualizations of your genomic data that give you the power to see what is occurring at each base pair in your samples. A high performance backend is paired with an user interface to make sure that your discovery process is fluid and streamlined. | Golden Helix, variant, visualization, genome |
is listed by: OMICtools has parent organization: Golden Helix Incorporated |
Free, Available for download, Freely available | OMICS_02129 | SCR_001213 | 2026-07-28 09:40:13 | 2 | ||||||||
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Mouse Brain Library Resource Report Resource Website 10+ mentions |
Mouse Brain Library (RRID:SCR_001112) | MBL | data or information resource, database, atlas, image collection, video resource, topical portal, portal | Collection of high resolution images and databases of brains from many genetically characterized strains of mice with aim to systematically map and characterize genes that modulate architecture of mammalian CNS. Includes detailed information on genomes of many strains of mice. Consists of images from approximately 800 brains and numerical data from just over 8000 mice. You can search MBL by strain, age, sex, body or brain weight. Images of slide collection are available at series of resolutions. Apple's QuickTime Plugin is required to view available MBL Movies. | brain, gene, genome, strain, c57bl/6j, dba/2j, a/j, genetic variant, phenotype, hippocampus, cerebellum, striatum, olfactory bulb, thalamus, neocortex, dorsal nucleus of lateral geniculate body, central nervous system |
is related to: Videoscribbler has parent organization: University of Tennessee Health Science Center; Tennessee; USA is parent organization of: MBL Pivot Collection is parent organization of: Mouse Brain Atlases |
NIMH P20 MH62009 | PMID:10857184 PMID:15043219 |
Restricted | nif-0000-00030 | SCR_001112 | MBL - Mouse Brain Library, Mouse Brain Library, The Mouse Brain Library | 2026-07-28 09:40:08 | 24 | |||||
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SynView Resource Report Resource Website 1+ mentions |
SynView (RRID:SCR_001106) | software application, data analysis software, sequence analysis software, software resource, data processing software | A software tool for comparative visualization of genomes. It is based in the GBrowse frameworks and integrates with the annotation features. | visualization, genome, comparison, gbrowse, sequence analysis software |
is used by: PlasmoDB is used by: ApiDB CryptoDB is listed by: OMICtools has parent organization: Generic Model Organism Database Project has parent organization: University of Georgia; Georgia; USA |
PMID:16844709 DOI:10.1093/bioinformatics/btl389 |
OMICS_00947 | SCR_001106 | 2026-07-28 09:40:08 | 1 | |||||||||
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SparseAssembler Resource Report Resource Website 1+ mentions |
SparseAssembler (RRID:SCR_001100) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software for memory-efficient genome assembly. It utilizes sparse k-mer. | genome, genomics, genome assembly, k-mer, sequence analysis software, memory |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22537038 | Free, Available for download, Freely available | OMICS_00032 | SCR_001100 | 2026-07-28 09:40:08 | 1 | ||||||||
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ChIP-seq Resource Report Resource Website 5000+ mentions |
ChIP-seq (RRID:SCR_001237) | ChIP-seq | software application, data analysis software, software resource, data processing software, software toolkit | Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well-defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface. | high-throughput sequencing, chromatin immuno precipitation, chip-seq, genome, c |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:27863463 | Free, Available for download, Freely available | OMICS_02103 | https://epd.expasy.org/chipseq/, https://chip-seq.sourceforge.net/ | SCR_001237 | ChIP-seq - Tools for the analysis of ChIP-seq data | 2026-07-28 09:40:13 | 7500 | |||||
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ALFRED Resource Report Resource Website 50+ mentions |
ALFRED (RRID:SCR_001730) | ALFRED | service resource, data or information resource, data repository, database, storage service resource | A public curated compilation of allele frequency data on anthropologically defined human population samples linked to the molecular genetics-human genome databases. Only data on well defined population samples that are large enough to yield reasonably accurate frequencies and for polymorphisms sufficiently defined to be replicable can be included in ALFRED. Researchers wishing to have their data entered into ALFRED should contact them. Initially, ALFRED contained primarily data generated in the laboratories of K.K. and J.R. Kidd in the Department of Genetics at Yale, including extensive unpublished data. Data from the published literature are being entered into ALFRED in a systematic way, with a focus on polymorphisms studied in many different populations. ALFRED is distinct from such databases as dbSNP, which catalogs sequence variation. ALFRED's focus is on allele frequencies in diverse anthropologically defined populations. It is not a compendium of human DNA polymorphisms but of frequencies of selected polymorphisms with an emphasis on those that have been studied in multiple populations. All of the data in ALFRED are considered to be in the public domain and available for use in research and teaching. ALFRED provides easy searching options including versatile "Keyword search" and also has numerous summary tables providing quick overviews of contents by chromosome, population, average heterozygosity, Fst and others, all available under various tabs from the ALFRED homepage. | allele frequency, dna polymorphism, haplotype, high throughput, genome, population, sample, education, polymorphism, allele, chromosome, heterozygosity, fst, loci, pathway, genetics, FASEB list | has parent organization: Yale School of Medicine; Connecticut; USA | NIGMS P01GM 57672 | PMID:19325849 PMID:11125124 PMID:12209575 |
Free, Freely Available | nif-0000-02541, r3d100012700 | https://doi.org/10.17616/R3GZ2J | SCR_001730 | The ALlele FREquency Database, ALlele FREquency Database | 2026-07-28 09:40:15 | 71 | ||||
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ASAP Resource Report Resource Website 50+ mentions |
ASAP (RRID:SCR_001849) | ASAP | service resource, data or information resource, data repository, database, storage service resource | Database and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene expression, genome, genome sequence, multiple genome sequence, post sequencing functional analysis, preliminary experiment, blast, annotation, data analysis service |
is used by: NIF Data Federation is listed by: SoftCite is related to: AmiGO has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
USDA 2001-52100-11316; NIGMS GM62994-02; NIGMS GM35682-15A1 |
PMID:12519969 | Free, Freely available | nif-0000-02571, r3d100010666 | https://omictools.com/asap-3-tool | SCR_001849 | A Systematic Annotation Package for Community Analysis of Genome, ASAP: a systematic annotation package for community analysis of genomes, A systematic annotation package for community analysis of genomes | 2026-07-28 09:40:17 | 53 | ||||
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TCAG Resource Report Resource Website 50+ mentions |
TCAG (RRID:SCR_001840) | TCAG | service resource, biomaterial analysis service, material service resource, data or information resource, database, production service resource, material analysis service, biomaterial manufacture, analysis service resource, topical portal, portal, training service resource | Service and training support for academic, government, and private sector scientists worldwide in genomics, including laboratory experimentation, statistical analysis, and comprehensive bioinformatics support, including large-scale genome comparisons, algorithm and tools development, and database curation, annotation and hosting. The Centre for Applied Genomics hosts a variety of databases related to ongoing supported projects: *Autism Chromosome Rearrangement Database *Cystic Fibrosis Mutation Database *The Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database *Database of Genomic Variants *The Chromosome 7 Annotation Project *Human Genome Segmental Duplication Database *Non-Human Segmental Duplication Database Healthy control DNA samples from the Ontario Population Genomics Platform are available. The Biobanking and Databasing Facility provides DNA extraction from lymphoblasts, fibroblasts and other cell types, archiving of white cell pellets, preparation and immortalization of cell lines, and comprehensive databasing and tracking of samples and/or cell lines within the facility. | genomics, publication, link, bioinformatics, genome, research, microarray analysis, gene expression, genotyping, biobanking, statistical analysis, genetic analysis, cytogenomics, dna sequencing, dna synthesis, comparative genomic hybridization, karyotyping, fish mapping, human, mouse, gene expression, biobanking, dna, mutation, genomic variant, chromosome 7, FASEB list | is listed by: One Mind Biospecimen Bank Listing | Healthy control, Autism, Cystic fibrosis, Epilepsy, Polymorphism | Free, Freely available | nif-0000-12519 | SCR_001840 | Centre for Applied Genomics, The Centre for Applied Genomics | 2026-07-28 09:40:26 | 80 | ||||||
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Generic Model Organism Database Project Resource Report Resource Website 1+ mentions |
Generic Model Organism Database Project (RRID:SCR_001731) | GMOD | data or information resource, database, software resource, topical portal, portal | A collection of open source software tools for creating and managing genome-scale biological databases. GMOD is made up databases, applications, and adaptor software that connects these components together. You can use it to create a small laboratory database of genome annotations, or a large web-accessible community database. At first GMOD just featured model organisms but now any organism with any kind of sequence associated with it is a good candidate as a subject for a GMOD database. There are GMOD databases with just protein sequence in them, with EST sequence only, those that are concerned primarily with gene expression, and even those dedicated to collections of RNA sequence. They have also heard of GMOD databases for oligonucleotides and plasmids. | genome, biological database, model organism, software, annotation, gene, sequence, expressed sequence tag, gene expression, rna sequence, oligonucleotide, plasmid |
is related to: Generic GO Term Mapper is related to: Generic GO Term Finder has parent organization: USDA Agricultural Research Service has parent organization: National Human Genome Research Institute has parent organization: National Institute of General Medical Sciences is parent organization of: SynView is parent organization of: Apollo is parent organization of: GBrowse is parent organization of: CMAP is parent organization of: GBrowse syn |
Free, Freely Available | nif-0000-10234 | SCR_001731 | Generic Model Organism Database | 2026-07-28 09:40:15 | 7 | |||||||
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Global Initiative on Sharing All Influenza Data Resource Report Resource Website 1000+ mentions |
Global Initiative on Sharing All Influenza Data (RRID:SCR_018251) | GISAID | disease-related portal, data or information resource, database, topical portal, portal | Portal to share hCoV-19 genome sequences. Collection of genome sequences and related clinical and epidemiological data associated with coronavirus hCoV-19. Global repository of SARS-CoV-2 genomes. Initiative involves public-private-partnerships between Freunde of GISAID and governments of Federal Republic of Germany, Singapore and United States of America, with support from private and corporate philanthropy.International database of hCoV-19 genome sequences and related clinical and epidemiological data. Resource for influenza and hCoV-19 data. | hCoV19, hCoV-19 genome sequence, data, coronavirus, SARS coronavirus, Coronavirus, genome, genome database, influenza, SARS-CoV infection, SARS-CoV-2, COVID-19 |
lists: Health Data Research UK COVID-19 Initiative is listed by: Data and Computational Resources to Address COVID-19 is related to: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation works with: Nextstrain |
CoV19, COVID19, COVID-19 | PMID:28382917 | Restricted | SCR_018279, r3d100010126, SCR_018318 | https://doi.org/10.17616/R3Q59F | SCR_018251 | 2026-07-28 09:44:39 | 1964 | |||||
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SARS-CoV-2-Sequences Resource Report Resource Website 10+ mentions |
SARS-CoV-2-Sequences (RRID:SCR_018319) | service resource, data set, data or information resource, data repository, storage service resource | Collection of SARS-CoV-2 sequences currently available in GenBank genetic sequence database and Sequence Read Archive. Updated as additional sequences are released. | SARS-CoV-2, SARS coronavirus, SARS-CoV infection, Coronavirus, data, SARS-CoV-2 sequence collection, nucleotide, genome, Betacoronavirus, protein |
works with: GenBank works with: NCBI Sequence Read Archive (SRA) |
COVID-19 | The Federal Government | Free, Available for download, Freely available | SCR_018319 | Severe Acute Respiratory Syndrome CoronaVirus 2 Sequences | 2026-07-28 09:44:54 | 28 | |||||||
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CRISPR-ERA Resource Report Resource Website 10+ mentions |
CRISPR-ERA (RRID:SCR_018710) | service resource, software resource, data access protocol, web service | Software comprehensive design tool for CRISPR mediated gene editing, repression and activation. Fast and comprehensive guide RNA design tool for genome editing, repression and activation. Used for automated genome wide sgRNA design. | Design tool, CRISPR mediated gene editing, gene repression, gene activation, guide RNA design, genome, automated genome, sgRNA design, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
NIH Office of The Director ; NIDCR ; NSFC ; FANEDD ; NIH Office of the Director OD017887; NIDA R01 DA036858 |
PMID:26209430 | Free, Freely available | biotools:CRISPR-ERA | https://bio.tools/CRISPR-ERA | SCR_018710 | CRISP-Editing, Repression and Activation | 2026-07-28 09:44:48 | 10 | |||||
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CaDBase: Genetic diversity in cattle Resource Report Resource Website 1+ mentions |
CaDBase: Genetic diversity in cattle (RRID:SCR_008146) | database, data or information resource, topical portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. The objective of the project is the standardization of micro-satellite markers used within participating laboratories, use of DNA markers to define genetic diversity and to enable monitoring of breeds to promote conservation programs where required, and the determination of diversity present in rare and local breeds across Europe. The blood typing laboratories are now beginning to use micro-satellite markers as an alternative to serology for parentage verification, and are selecting a common set to be used from the several hundred micro-satellite markers available that cover the bovine genome, produced as part of the Bovine genome mapping project (See BovMaP). Work with micro-satellite markers has shown that they are valuable tools for examining genetic diversity and phylogeny in many species. However, for work carried out in different laboratories to be comparable, it is essential that the same markers are used. To maintain the compatibility of data generated by the various typing labs, it is essential that all laboratories adopt the same markers and typing protocols. It is therefore of paramount importance that the blood typing laboratories and research labs that are examining the genetic structure of the cattle populations adopt a common panel of the best micro-satellite markers available. Some pilot comparative work has been undertaken through the International Society for Animal Genetics, but so far this has only involved the blood typing laboratories. One objective of this project is to facilitate the comparison of the micro-satellite markers currently in use in the different types of laboratory and determine the efficiency of the markers available in revealing genetic differences within and among breeds. It will also be important to compare the use of markers in different laboratories to determine how robust they are and how easily results can be compared. From comparison of the markers, those that are most suitable will be selected to form a panel which will be recommended for pedigree validation and genetic surveys. Cattle are an important source of food in Europe, and intense selection has resulted in the development of specialized breeds. Selection for high-producing dairy cattle has been successful, but one associated drawback is that the cattle population, both in Europe and North America, has been skewed dramatically towards one breed, the Holstein/Friesian. So there has been a decline in the number of individuals of other breeds, and hence a general erosion of the genetic base of the cattle population. The progressive move towards the North American-type Holstein animals has also resulted in the requirement for high input/high output farming and intensive management schemes. The impact of this on the environment has been significant, e.g. pollution problems arising from the need for high nitrogen fertilizers to produce sufficient high quality fodder, and disposal problems associated with slurry waste. Poorer areas of the community have been unable to compete with such farming systems, and are more suited to low input/low output farming using traditional stock. It is however the future perspective that is of greatest concern. It is impossible to predict requirements for cattle production - quality, production type, management systems, etc. The ability to switch rapidly to alternative production will be dependent on the genetic base of the population available to selection programs. It is therefore essential to maintain the greatest genetic diversity possible in the cattle population. Whilst current farming practices are perceived to be both efficient and acceptable, the breeds less favored by commercial farmers will dwindle. It is therefore important that on an European scale efficient management of these breeds maintains the widest genetic base possible. This project aims to carry out a survey of the current genetic base of the European cattle population and to provide the tools to assist breeding programs to maintain a broad base. The blood typing laboratories are now beginning to use micro-satellite markers as an alternative to serology for parentage verification, and are selecting a common set to be used from the several hundred micro-satellite markers available that cover the bovine genome, produced as part of the Bovine genome mapping project. Early work to measure genetic diversity used blood groups to show differences between breeds and the diversity present. Unfortunately, the number of loci available are limited, with only the B system being sufficiently polymorphic to be really useful. However, since there is a wealth of information available from such typing, this information can be used to estimate changes in the genetic structure of cattle populations across Europe over the past twenty years. More recently mini-satellite probes have been used to generate ''genetic fingerprints'' which have been used to show differences between individuals. Such fingerprints have been used to estimate genetic diversity - the greater the number of bands revealed by the fingerprint being equated with greater diversity. This is valid within limits. The main disadvantage of the fingerprint approach is that the chromosomal location and number of loci being sampled, and so the proportion of the genome examined, is unknown. The allelic bands on the gel cannot be easily identified, so allele inheritance cannot be addressed making it impossible to trace ancestry. Through the EC funded BovMaP project, large numbers of highly polymorphic micro-satellite markers have become available, which are being mapped on the bovine genome. These markers are particularly suited to measuring genetic diversity, and markers can be selected to cover the entire genome. | micro-satellite, dna, genetic, diversity, breed, conservation, pedigree, cattle, bovine, cow, blood, typing, serology, parentage, mapping, genome, marker, genetic, structure, population, animal, holstein, farming, fertilizer, locus, polymorphic, allelic, ancestry, people resource | has parent organization: University of Edinburgh; Scotland; United Kingdom | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20969 | SCR_008146 | Genetic diversity in cattle | 2026-07-28 09:42:01 | 1 | ||||||||
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BovMap Database Resource Report Resource Website 1+ mentions |
BovMap Database (RRID:SCR_008145) | BovMap | service resource, data or information resource, data repository, database, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database containing information on the cattle genome comprising loci list, phenes list, homology query, cattle maps, gene list, and chromosome homology. The objective of BovMap is to develop a set of anchored loci for the cattle genome map. In total, 58 clones were hybridized with chromosomes and identified loci on 22 of the 31 different bovine chromosomes. Three clones contained satellite DNA. Two or more markers were placed on 12 chromosomes. Sequencing of the microsatellites and flanking regions was performed directly from 43 cosmids, as previously reported. Primers were developed for 39 markers and used to describe the polymorphism associated with the corresponding loci. Users are also allowed to summit their own data for Bovmap. An integrated cytogenetic and meiotic map of the bovine genome has also been developed around the Bovmap database. One objective that Bovmap uses as the mapping strategy for the bovine genome uses large insert clones as a tool for physical mapping and as a source of highly polymorphic microsatellites for genetic typing. | genetic, bovine, cattle, chromosome, clone, cosmid, cow, cytogenetic, dna, genome, homology, locus, meiotic, phene, polymorphism, sequence, map, gene | has parent organization: INRA - French National Institute for Agricultural Research; Paris; France | European Union | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20968 | SCR_008145 | 2026-07-28 09:42:17 | 2 | |||||||
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E. coli Genome project Resource Report Resource Website 1+ mentions |
E. coli Genome project (RRID:SCR_008139) | database, data or information resource, topical portal, portal | The E. coli Genome Project has the goal of completely sequencing the E. coli and human genomes. They began isolation of an overlapping lambda clonebank of E. coli K-12 strain MG1655. Those clones served as the starting material in our initial efforts to sequence the whole genome. Improvements in sequencing technology have since reached the point where whole-genome sequencing of microbial genomes is routine, and the human genome has in fact been completed. They initiated additional sequencing efforts, concentrating on pathogenic members of the family Enterobacteriaceae -- to which E. coli belongs. They also began a systematic functional characterization of E. coli K-12 genes and their regulation, using the whole genome sequence to address how the over 4000 genes of this organism act together to enable its survival in a wide range of environments. | e. coli, enterobcteriaceae, gene, genome, human, journal aricle, knowledgebase, regulation, sequence, job | has parent organization: University of Wisconsin-Madison; Wisconsin; USA | NIAID ; NHGRI |
nif-0000-20961 | SCR_008139 | E.Coli genome project | 2026-07-28 09:42:17 | 5 | ||||||||
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MitoRes Resource Report Resource Website 1+ mentions |
MitoRes (RRID:SCR_008208) | MitoRes | software application, data analysis software, software resource, data processing software, data acquisition software | MitoRes, is a comprehensive and reliable resource for massive extraction of sequences and sub-sequences of nuclear genes and encoded products targeting mitochondria in metazoa. It has been developed for supporting high-throughput in-silico analyses aimed to studies of functional genomics related to mitochondrial biogenesis, metabolism and to their pathological dysfunctions. It integrates information from the most accredited world-wide databases to bring together gene, transcript and encoded protein sequences associated to annotations on species name and taxonomic classification, gene name, functional product, organelle localization, protein tissue specificity, Enzyme Classification (EC), Gene Ontology (GO) classification and links to other related public databases. The section Cluster, has been dedicated to the collection of data on protein clustering of the entire catalogue of MitoRes protein sequences based on all versus all global pair-wise alignments for assessing putative intra- and inter-species functional relationships. The current version of MitoRes is based on the UniProt release 4 and contains 64 different metazoan species. The incredible explosion of knowledge production in Biology in the past two decades has created a critical need for bioinformatic instruments able to manage data and facilitate their retrieval and analysis. Hundreds of biological databases have been produced and the integration of biological data from these different resources is very important when we want to focus our efforts towards the study of a particular layer of biological knowledge. MitoRes is a completely rebuilt edition of MitoNuc database, which has been extensively modified to deal successfully with the challenges of the post genomic era. Its goal is to represent a comprehensive and reliable resource supporting high-quality in-silico analyses aimed to the functional characterization of gene, transcript and amino acid sequences, encoded by the nuclear genome and involved in mitochondrial biogenesis, metabolism and pathological dysfunctions in metazoa. The central features of MitoRes are: # an integrated catalogue of protein, transcript and gene sequences and sub-sequences # a Web-based application composed of a wide spectrum of search/retrieval facilities # a sequence export manager allowing massive extraction of bio-sequences (genes, introns, exons, gene flanking regions, transcripts, UTRs, CDS, proteins and signal peptides) in FASTA, EMBL and GenBank formats. It is an interconnected knowledge management system based on a MySQL relational database, which ensures data consistency and integrity, and on a Web Graphical User Interface (GUI), built in Seagull PHP Framework, offering a wide range of search and sequence extraction facilities. The database is compiled extracting and integrating information from public resources and data generated by the MitoRes team. The MitoRes database consists of comprehensive sequence entries whose core data are protein, transcript and gene sequences and taxonomic information describing the biological source of the protein. Additional information include: bio-sequences structure and location, biological function of protein product and dynamic links to both, external public databases used as data resources and public databases reporting complementary information. The core entity of the MitoRes database is represented by the protein so that each MitoRes entry is generated for each protein reported in the UniProt database as a nuclear encoded protein involved in mitochondrial biogenesis and function. Sponsors: MitoRes has been supported by Ministero Universit e Ricerca Scientifica, Italy (PRIN, Programma Biotecnologie legge 95/95-MURST 5, Proiect MURST Cluster C03/2000, CEGBA). Currently it is supported by operating grants from the Ministero dellIstruzione, dellUniversit e della Ricerca (MIUR), Italy (PNR 2001-2003 (FIRB art.8) D.M. 199, Strategic Program: Post-genome, grant 31-063933 and Project n.2, Cluster C03 L. 488/929). | dysfunction, encode, enzyme, exon, extraction, function, functional, gene, alignment, amino acid, biogenesis, bioinformatic, biological, biology, cds, classification, disfunctional, genome, genomic, genomics, intron, localization, location, metabolic process, metabolism, metazoa, mitochondria, mitochondrial, mitochondrial genes and proteins databases, nuclear, nuclear_gene, nuclear_mitochondrial, nuclear_sequence, organelle, organelle localization, pathological, peptide, protein, protein_coding, protein structure classification, region, sequence, signal, signal_peptide, specie, specificity, structure, sub-sequence, taxonomic, tissue, transcript, utr | nif-0000-21269 | http://www2.ba.itb.cnr.it/MitoNuc/ | SCR_008208 | 2026-07-28 09:42:05 | 1 | |||||||||
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Parasite genome databases and genome research resources Resource Report Resource Website 1+ mentions |
Parasite genome databases and genome research resources (RRID:SCR_008150) | database, data or information resource, topical portal, portal | This website contains information about the genomic sequence of parasites. It also contains multiple search engines to search six frame translations of parasite nucleotide databases for motifs, parasite protein databases for motifs, and parasite protein databases for keywords and text terms. * Guide to Internet Access to Parasite Genome Information * Guide to web-based analysis tools * Parasite Genome BLAST Server: Search a range of parasite specific nucleotide sequence databases with your own sequence. * Parasite Proteome Keyword Search Facility: Search parasite protein databases for keywords and text terms * Parasite Proteome Motif Search Facility: Search parasite protein databases for motifs * Parasite Six Frame Translation Motif Search Facility: Search six frame translations of parasite nucleotide databases for motifs * Genome computing resources: A list of ftp and gopher sites where genome computing applications and other resources can be found. | genome, genomic, nucleotide, parasite, protein, proteome, sequence, gold standard | has parent organization: European Bioinformatics Institute | nif-0000-20981 | SCR_008150 | Parasite Genome Database | 2026-07-28 09:42:01 | 2 |
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