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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NOVOPlasty Resource Report Resource Website 100+ mentions |
NOVOPlasty (RRID:SCR_017335) | software application, data processing software, image analysis software, software resource, alignment software | Software package as de novo assembler and heteroplasmy variance caller for short circular genomes. Used for de novo assembly of organelle genomes from whole genome data. | de novo, assembler, heteroplasmy, variance, caller, short, circular, genome, organelle, whole, data | is listed by: OMICtools | Interuniversity Institute of Bioinformatics in Brussels ; Belgian Kids Fund ; Hôpital Universitaire des Enfants Reine Fabiola |
PMID:28204566 | Free, Available for download, Freely available | SCR_017335 | 2026-02-16 09:49:13 | 161 | ||||||||
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miRquant Resource Report Resource Website 1+ mentions |
miRquant (RRID:SCR_017261) | software application, data processing software, data analytics software, data analysis software, software resource | Software tool for accurate annotation and quantification of microRNAs and their isomiRs from small RNA-sequencing data. Provides information on quality of sequencing data, genome mapping statistics, abundance of other types of small RNAs such as tDRs and yDRs, prevalence of post transcriptional modifications. | annotation, quantification, miRNA, smRNA-seq, data, functionally, distinct, isoform, isomiR, quality, sequencing, genome, mapping, statistic, tDR, yDR | PMID:28187421 | Free, Available for download, Freely available | SCR_017261 | miRquant 2.0 | 2026-02-16 09:49:12 | 1 | |||||||||
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Animal Genome Size Database Resource Report Resource Website 100+ mentions |
Animal Genome Size Database (RRID:SCR_007551) | Genomesize | data repository, database, storage service resource, catalog, service resource, data or information resource | Comprehensive catalogue of animal genome size data. Haploid DNA contents (C-values, in picograms) are available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources. Data may be submitted directly to the database or reprints and notifications of new papers may be sent to database curation staff. | genome size, haploid dna, non-vertebrate, vertebrate, genome structure, comparative biodiversity, sequencing, genome, genomic, FASEB list | has parent organization: University of Guelph; Ontario; Canada | Natural Sciences and Engineering Research Council of Canada | PMID:17090588 | Data taken from the database must not be reproduced in published lists, Online databases, Or other such formats, Nor redistributed without permission. The information is provided solely for personal and academic use., Please cite, The community can contribute to this resource | nif-0000-02548, r3d100012517 | https://doi.org/10.17616/R3R782 https://doi.org/10.17616/R3R782 |
SCR_007551 | 2026-02-16 09:47:00 | 173 | |||||
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Gene3D Resource Report Resource Website 100+ mentions |
Gene3D (RRID:SCR_007672) | Gene3D | web service, data access protocol, data repository, database, storage service resource, software resource, service resource, data or information resource | A large database of CATH protein domain assignments for ENSEMBL genomes and Uniprot sequences. Gene3D is a resource of form studying proteins and the component domains. Gene3D takes CATH domains from Protein Databank (PDB) structures and assigns them to the millions of protein sequences with no PDB structures using Hidden Markov models. Assigning a CATH superfamily to a region of a protein sequence gives information on the gross 3D structure of that region of the protein. CATH superfamilies have a limited set of functions and so the domain assignment provides some functional insights. Furthermore most proteins have several different domains in a specific order, so looking for proteins with a similar domain organization provides further functional insights. Strict confidence cut-offs are used to ensure the reliability of the domain assignments. Gene3D imports functional information from sources such as UNIPROT, and KEGG. They also import experimental datasets on request to help researchers integrate there data with the corpus of the literature. The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes. Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins. The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | protein domain, protein, protein superfamily, hidden markov model, structural domain, genome, sequence, domain assignments, protein structure, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University College London; London; United Kingdom |
NIH ; Wellcome Trust ; European Union FP6 ENFIN LSHG-CT-2003-503265; European Union FP6 ENFIN LSHG-CT-2004-512092; European Union FP6 ENFIN LSHG-CT-2005-518254; DOE DE-AC02-065CH11357 |
PMID:19906693 PMID:18032434 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02877, biotools:gene3d | https://bio.tools/gene3d | SCR_007672 | Gene3D - Structures assigned to Genomes | 2026-02-16 09:47:01 | 272 | ||||
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Human Ageing Genomic Resources Resource Report Resource Website 50+ mentions |
Human Ageing Genomic Resources (RRID:SCR_007700) | HAGR | data or information resource, database, software toolkit, software resource | Collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses. A major resource in HAGR is GenAge, which includes a curated database of genes related to human aging and a database of ageing- and longevity-associated genes in model organisms. Another major database in HAGR is AnAge. Featuring over 4,000 species, AnAge provides a compilation of data on aging, longevity, and life history that is ideal for the comparative biology of aging. GenDR is a database of genes associated with dietary restriction based on genetic manipulation experiments and gene expression profiling. Other projects include evolutionary studies, genome sequencing, cancer genomics, and gene expression analyses. The latter allowed them to identify a set of genes commonly altered during mammalian aging which represents a conserved molecular signature of aging. Software, namely in the form of scripts for Perl and SPSS, is made available for users to perform a variety of bioinformatic analyses potentially relevant for studying aging. The Perl toolkit, entitled the Ageing Research Computational Tools (ARCT), provides modules for parsing files, data-mining, searching and downloading data from the Internet, etc. Also available is an SPSS script that can be used to determine the demographic rate of aging for a given population. An extensive list of links regarding computational biology, genomics, gerontology, and comparative biology is also available. | gene, gerontology, human, model, senescence, genomics, longevity, genetics, perl, spss, demographic analysis, genome, evolution, gene expression, model organism, human aging, dietary restriction, genetic manipulation |
has parent organization: University of Liverpool; Liverpool; United Kingdom is parent organization of: anage is parent organization of: GenAge |
Aging, Cancer | Ellison Medical Foundation ; Wellcome Trust ME050495MES; European Union FP7 Health Research HEALTH-F4-2008-202047 |
PMID:23193293 | GNU General Public License, Creative Commons Attribution v3 Unported License | nif-0000-02938, r3d100011871 | https://doi.org/10.17616/R34W81 | SCR_007700 | 2026-02-16 09:47:01 | 67 | ||||
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GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database Resource Report Resource Website 1+ mentions |
GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database (RRID:SCR_007440) | GEISHA | narrative resource, experimental protocol, atlas, data repository, database, storage service resource, service resource, data or information resource | Online repository for chicken in situ hybridization information. This site presents whole mount in situ hybridization images and corresponding probe and genomic information for genes expressed in chicken embryos in Hamburger Hamilton stages 1-25 (0.5-5 days). The GEISHA project began in 1998 to investigate using high throughput whole mount in situ hybridization to identify novel, differentially expressed genes in chicken embryos. An initial expression screen of approximately 900 genes demonstrated feasibility of the approach, and also highlighted the need for a centralized repository of in situ hybridization expression data. Objectives: The goals of the GEISHA project are to obtain whole mount in situ hybridization expression information for all differentially expressed genes in the chicken embryo between HH stages 1-25, to integrate expression data with the chicken genome browsers, and to offer this information through a user-friendly graphical user interface. In situ hybridization images are obtained from three sources: 1. In house high throughput in situ hybridization screening: cDNAs obtained from several embryonic cDNA libraries or from EST repositories are screened for expression using high throughput in situ hybridization approaches. 2. Literature curation: Agreements with journals permit posting of published in situ hybridization images and related information on the GEISHA site. 3. Unpublished in situ hybridization information from other laboratories: laboratories generally publish only a small fraction of their in situ hybridization data. High quality images for which probe identity can be verified are welcome additions to GEISHA. | expression data, expression pattern, gene, gene expression, genome, chicken, chicken embryo, genomic, in situ hybridization, mapping, microarray, microrna, model organism, oligo, probe, stage, image, molecular neuroanatomy resource, embryo, embryonic chicken | has parent organization: University of Arizona; Arizona; USA | NIH ; NICHD R01HD044767 |
nif-0000-01251, r3d100012509 | https://doi.org/10.17616/R3RB6B | SCR_007440 | Gallus Expression in Situ Hybridization Analysis, GEISHA - Gallus Expression in Situ Hybridization Analysis | 2026-02-16 09:46:58 | 2 | ||||||
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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 | 2026-02-16 09:47:07 | 1 | ||||||||
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BovMap Database Resource Report Resource Website 1+ mentions |
BovMap Database (RRID:SCR_008145) | BovMap | data repository, database, storage service resource, service resource, data or information 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 | 2026-02-16 09:47:07 | 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 | 2026-02-16 09:47:07 | 5 | ||||||||
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MitoRes Resource Report Resource Website 1+ mentions |
MitoRes (RRID:SCR_008208) | MitoRes | software application, data processing software, data analysis software, software resource, 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 | 2026-02-16 09:47:08 | 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 | 2026-02-16 09:47:07 | 2 | |||||||||
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REBASE Resource Report Resource Website 100+ mentions |
REBASE (RRID:SCR_007886) | REBASE | database, data or information resource | Database of information about restriction enzymes and related proteins containing published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Several tools are available including REBsites, BLAST against REBASE, NEBcutter and REBpredictor. Putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. REBASE is updated daily and is constantly expanding. Users may submit new enzyme and/or sequence information, recommend references, or send them corrections to existing data. The contents of REBASE may be browsed from the web and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email., | endonuclease, enzyme, genome, archaeal, bacterial, cleavage, crystal, dna, individual protein family databases, isochizomer, methylation, methyltransferase, modification, protein, recognition, restriction, restriction enzyme, sensitivity, sequence, site, methylase, cleavage site, restriction-modification, blast, FASEB list |
has parent organization: New England Biolabs works with: Webcutter |
New England Biolabs Inc ; NLM LM04971 |
PMID:19846593 PMID:17202163 |
r3d100012171, nif-0000-03391 | http://rebase.neb.com https://doi.org/10.17616/R3J930 |
http://www.neb.com/rebase | SCR_007886 | The Restriction Enzyme Database, Restriction Enzyme Database | 2026-02-16 09:47:03 | 246 | ||||
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Dog Genome Project Resource Report Resource Website 1+ mentions |
Dog Genome Project (RRID:SCR_008486) | data or information resource, topical portal, portal | The genome of the domesticated dog, a close evolutionary relation to human, is a powerful new tool for understanding the human genome. Comparison of the dog with human and other mammals reveals key information about the structure and evolution of genes and genomes. The unique breeding history of dogs, with their extraordinary behavioral and physical diversity, offers the opportunity to find important genes underlying diseases shared between dogs and humans, such as cancer, diabetes, and epilepsy. The Canine Genome Sequencing Project produced a high-quality draft sequence of a female boxer named Tasha. By comparing Tasha with many other breeds, the project also compiled a comprehensive set of SNPs (single nucleotide polymorphisms) useful in all dog breeds. These closely spaced genomic landmarks are critical for disease mapping. By comparing the dog, rodent, and human lineages, researchers at the Broad Institute uncovered exciting new information about human genes, their evolution, and the regulatory mechanisms governing their expression. Using SNPs, researchers describe the strikingly different haplotype structure in dog breeds compared with the entire dog population. In addition, they show that by understanding the patterns of variation in dog breeds, scientists can design powerful gene mapping experiments for complex diseases that are difficult to map in human populations. Contribute Although the astounding generosity of Eli and Edythe L. Broad and several other venture philanthropists empowers our scientists to tackle many of the most important problems at the cutting edge of genomic medicine, there are many other critical challenges that they cannot yet pursue because of limited resources. We need additional visionary partners to join the Broads and the Broad Institute in transforming medicine with the power of genomics. | dog, canine, human, gene, medical, research, genome, annotation | has parent organization: Broad Institute | NIH Office of the Director R24 OD018250 | nif-0000-30464 | http://dogdata.org/ https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources https://www.broadinstitute.org/mammals-models/broad-institute-canine-genomic-resources |
SCR_008486 | Dog Genome, Canine Genome Project, Dog Gene Project, A Comprehensive Canine Genetics Resource Including Gene and Variation Annotation, Dog Genetics Project | 2026-02-16 09:47:12 | 4 | |||||||
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Bovine Genome Project Resource Report Resource Website |
Bovine Genome Project (RRID:SCR_008370) | Bovine Genome Project | data set, data analysis service, analysis service resource, production service resource, service resource, data or information resource | Downloadable files of the bos taurus genome. Draft assemblies available for download as contigs or linearized scaffolds of the genomic sequence of cow, Bos taurus, including the final draft assembly (7.1 coverage) and the two previous assemblies. The genome is sequenced to 6- to 8-fold sequence depth, with high-quality finished sequence in some areas. Accompanying EST and SNP analyses is also included. The bovine genome assembly and analysis and the study of cattle genetic history were published in April 24, 2009 issue of Science. The Human Genome Sequencing Center provides BLAST searches of the genome assemblies, either as contigs or as linearized chromosome sequences. The WGS sequence enriched BAC assemblies and the unassembled reads (sequencing reads that did not end up in the genome assembly) can also be searched by BLAST. Traces are available from the NCBI Trace Archive by using the link in the sidebar or by using NCBI MegaBLAST with a same species or cross species query. | bovine, cattle, cow, genome, genotype, reagent, sequencing, blast, genome assembly, contig, linearized chromosome, single nucleotide polymorphism, bac map, expressed sequence tag | has parent organization: Baylor University; Texas; USA | NHGRI ; USDA Agricultural Research Service ; USDA Cooperative State Research Education and Extension Service ; State of Texas ; Genome Canada ; Genome British Columbia ; CSIRO ; Agritech Investments Ltd. New Zealand ; Dairy Insight Inc. New Zealand ; AgResearch Ltd.New Zealand ; Robert J. Kleberg ; Jr. and Helen C. Kleberg Foundation ; National Texas and South Dakota Beef Check-off Funds |
PMID:19393050 | nif-0000-25603 | http://www.hgsc.bcm.tmc.edu/project-species-m-Bovine.hgsc?pageLocation=Bovine | SCR_008370 | 2026-02-16 09:47:10 | 0 | ||||||
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Rat Genome Database: Neurological Disease Portal Resource Report Resource Website 10+ mentions |
Rat Genome Database: Neurological Disease Portal (RRID:SCR_008685) | data or information resource, topical portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Portal that provides researchers with easy access to data on rat genes, QTLs, strain models, biological processes and pathways related to neurological diseases. This resource also includes dynamic data analysis tools. | gene, analysis, biological, data, database, disease, genome, model, neurological, neuroscience, pathway, phenotype, qtl, rat, research | has parent organization: Medical College of Wisconsin; Wisconsin; USA | Neurological disease | RGD ; NINDS |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33773 | http://rgd.mcw.edu | SCR_008685 | RGD Neurological Disease Portal | 2026-02-16 09:47:14 | 14 | |||||
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SCPD - Saccharomyces cerevisiae promoter database Resource Report Resource Website 10+ mentions |
SCPD - Saccharomyces cerevisiae promoter database (RRID:SCR_004412) | SCPD | data analysis service, analysis service resource, data repository, database, storage service resource, production service resource, service resource, data or information resource | A promoter database of Saccharomyces cerevisiae. Users can explore the promoter regions of ~6000 genes and ORFs in yeast genome, annotate putative regulatory sites of all genes and ORFs, locate intergenic regions, and retrieve sequence of the promoter region. In regards to regulatory elements and transcription factors, users can provide information on transcriptionally related genes, browse matrix and consensus sequences, view the correlation between elements, observe binding affinity and expression, and look at genomewise distribution. SCPD also provides some simple but useful tools for promoter sequence analysis. Gene, consensus and matrix records may be submitted. | promoter, gene, genome, orf, transcription factor binding site, transcriptional start site, transcription factor |
is listed by: OMICtools has parent organization: Cold Spring Harbor Laboratory |
PMID:10487868 | OMICS_01867, nif-0000-03445 | SCR_004412 | SCPD - The Promoter Database of Saccharomyces cerevisiae | 2026-02-16 09:46:19 | 20 | |||||||
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SO Resource Report Resource Website 10+ mentions |
SO (RRID:SCR_004374) | SO | ontology, data or information resource, controlled vocabulary | A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl. | annotation, sequence, biological sequence, sequence variation, genome, genome annotation, owl, FASEB list |
is listed by: BioPortal is related to: ASOoViR is related to: VAGrENT has parent organization: OBO has parent organization: Gene Ontology |
NHGRI HG02273 | PMID:20796305 PMID:20226267 PMID:18629179 PMID:15892872 |
The community can contribute to this resource | nlx_38918 | SCR_004374 | Sequence Ontology Project, Sequence Types and Features Ontology, Sequence Ontology | 2026-02-16 09:46:22 | 44 | |||||
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Velvet-SC Resource Report Resource Website 1+ mentions |
Velvet-SC (RRID:SCR_004377) | Velvet SC | software application, data processing software, sequence analysis software, data analysis software, software resource | Software package for short read data from single cells that improves assembly through use of progressively increasing coverage cutoff. Used for single cell Illumina sequences, allows variable coverage datasets to be utilized with assembly of E. coli and S. aureus single cell reads. Assembles single cell genome of uncultivated SAR324 clade of Deltaproteobacteria. | genome, single, cell, short, read, assembly |
is listed by: OMICtools is related to: Velvet has parent organization: University of California at San Diego; California; USA |
NHGRI R01 HG003647; Sloan Foundation ; NCRR P41 RR024851 |
PMID:21926975 | Free, Available for download, Freely available | OMICS_01504 | SCR_004377 | Velvet Single Cell | 2026-02-16 09:46:16 | 5 | |||||
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GeneDB Lmajor Resource Report Resource Website 1+ mentions |
GeneDB Lmajor (RRID:SCR_004613) | GeneDB_Lmajor, GeneDB Lmajor, GeneDB L. major, | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | Database of the most recent sequence updates and annotations for the L. major genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The Pathogen Genomics group at the Wellcome Trust Sanger Institute played a major role in sequencing the genome of Leishmania major (see Ivens et al.) Details of the centres involved and which chromosomes they sequenced, are given. The sequence data were obtained by adopting several parallel approaches, including complete cosmid sequencing, whole chromosome shotguns and/or BAC sequencing/skimming. The Leishmania parasite is an intracellular pathogen of the immune system targeting macrophages and dendritic cells. The disease Leishmaniasis affects the populations of 88 counties worldwide with symptoms ranging from disfiguring cutaneous and muco-cutaneous lesions that can cause widespread destruction of mucous membranes to visceral disease affecting the haemopoetic organs. In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries. | genome, gene, rna gene, rna, pseudogene, protein-coding, function, host-pathogen interaction, interaction, proteolytic enzyme, glycoconjugate, sequence annotation |
is used by: NIF Data Federation is related to: AmiGO is related to: TriTrypDB has parent organization: GeneDB |
Wellcome Trust | PMID:16020728 | nlx_60997 | SCR_004613 | Leishmania major strain Friedlin, Leishmania major strain Friedlin homepage on GeneDB, GeneDB Leishmania major, Leishmania major strain Friedlin on GeneDB | 2026-02-16 09:46:23 | 7 | ||||||
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NCBI BLAST Resource Report Resource Website 10000+ mentions |
NCBI BLAST (RRID:SCR_004870) | BLAST | software application, data processing software, web service, sequence analysis software, data analysis software, data access protocol, software resource | Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences. | genome, similarity, sequence, nucleotide, protein, gene, data, bio.tools |
is used by: MITE-Tracker is used by: Cello2Go is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: G-BLASTN is related to: genBlastA has parent organization: NCBI is required by: RelocaTE works with: Whole Genome Shotgun (WGS) Project works with: BLASTClust works with: MOLE-BLAST works with: Genotyping |
National Library of Medicine | PMID:16845079 PMID:18440982 |
Free, Freely available, Tutorial available | OMICS_01436, nlx_84530, biotools:blast | http://blast.ncbi.nlm.nih.gov https://bio.tools/blast https://sources.debian.org/src/ncbi-blast+/ |
SCR_004870 | NCBI Basic Local Alignment Search Tool, NCBI BLAST, Basic Local Alignment Search Tool, BLAST | 2026-02-16 09:46:20 | 15381 |
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