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http://www.knockoutmouse.org/

Database of the international consortium working together to mutate all protein-coding genes in the mouse using a combination of gene trapping and gene targeting in C57BL/6 mouse embryonic stem (ES) cells. Detailed information on targeted genes is available. The IKMC includes the following programs: * Knockout Mouse Project (KOMP) (USA) ** CSD, a collaborative team at the Children''''s Hospital Oakland Research Institute (CHORI), the Wellcome Trust Sanger Institute and the University of California at Davis School of Veterinary Medicine , led by Pieter deJong, Ph.D., CHORI, along with K. C. Kent Lloyd, D.V.M., Ph.D., UC Davis; and Allan Bradley, Ph.D. FRS, and William Skarnes, Ph.D., at the Wellcome Trust Sanger Institute. ** Regeneron, a team at the VelociGene division of Regeneron Pharmaceuticals, Inc., led by David Valenzuela, Ph.D. and George D. Yancopoulos, M.D., Ph.D. * European Conditional Mouse Mutagenesis Program (EUCOMM) (Europe) * North American Conditional Mouse Mutagenesis Project (NorCOMM) (Canada) * Texas A&M Institute for Genomic Medicine (TIGM) (USA) Products (vectors, mice, ES cell lines) may be ordered from the above programs.

Proper citation: International Knockout Mouse Consortium (RRID:SCR_005574) Copy   

•   Source: SciCrunch Registry

http://swissregulon.unibas.ch/fcgi/sr/swissregulon

A database of genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including: * Experimentally determined binding sites reported in the literature. * Known sequence-specificities of transcription factors. * ChIP-chip and ChIP-seq data. * Alignments of orthologous non-coding regions. Predictions were made using the PhyloGibbs, MotEvo, IRUS and ISMARA algorithms developed in their group, depending on the data available for each organism. Annotations can be viewed in a Gbrowse genome browser and can also be downloaded in flat file format.

Proper citation: SwissRegulon (RRID:SCR_005333) Copy   

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http://transpogene.tau.ac.il/

A publicly available database of Transposed elements (TEs) which are located within protein-coding genes of 7 organisms: human, mouse, chicken, zebrafish, fruilt fly, nematode and sea squirt. Using TranspoGene the user can learn about the many aspects of the effect these TEs have on their hosting genes, such as: exonization events (including alternative splicing-related data), insertion of TEs into introns, exons, and promoters, specific location of the TE over the gene, evolutionary divergence of the TE from its consensus sequence and involvement in diseases. TranspoGene database is quickly searchable through its website, enables many kinds of searches and is available for download. TranspoGene contains information regarding specific type and family of the TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern. The TranspoGene and microTranspoGene databases can be used by researchers interested in the effect of TE insertion on the eukaryotic transcriptome.

Proper citation: TranspoGene (RRID:SCR_005634) Copy   

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http://bigg.ucsd.edu/

A knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.

Proper citation: BiGG Database (RRID:SCR_005809) Copy   

•   Source: SciCrunch Registry

http://h-invitational.jp/varygene/

It consists of a Genome Browser, an LD Search System, and the VaryGene 2 system. The Generic Genome Browser is a combination of database and interactive Web page for manipulating and displaying annotations on genomes, while LDSearchSystem is a search system for linkage disequilibrium (LD) bins. VaryGene 2 is a system to search, display, and download our research results on human polymorphism based on publicly available data and annotations of transcripts presented by H-InvDB. VaryGene 2 provides information about single nucleotide polymorphisms (SNPs), deletion-insertion polymorphisms (DIPs), short tandem repeats (STRs), single amino acid repeats (SARs), structural variation (or copy number variations: CNVs), and their relations to the genome, transcripts, and functional domains. Users can search by polymorphisms, transcripts, STRs/SARs, and CNVs.

Proper citation: VarySysDB (RRID:SCR_005880) Copy   

•   Source: SciCrunch Registry

http://yh.genomics.org.cn

This database presents the entire DNA sequence of the first diploid genome sequence of a Han Chinese, a representative of Asian population. The genome, named as YH, represents the start of YanHuang Project, which aims to sequence 100 Chinese individuals in 3 years. It was assembled based on 3.3 billion reads (117.7Gbp raw data) generated by Illumina Genome Analyzer. In total of 102.9Gbp nucleotides were mapped onto the NCBI human reference genome (Build 36) by self-developed software SOAP (Short Oligonucleotide Alignment Program), and 3.07 million SNPs were identified. The personal genome data is illustrated in a MapView, which is powered by GBrowse. A new module was developed to browse large-scale short reads alignment. This module enabled users track detailed divergences between consensus and sequencing reads. In total of 53,643 HGMD recorders were used to screen YH SNPs to retrieve phenotype related information, to superficially explain the donor's genome. Blast service to align query sequences against YH genome consensus was also provided.

Proper citation: YanHuang Project (RRID:SCR_006077) Copy   

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http://ygac.med.yale.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. TRIPLES provides full public access to the data and reagents generated from ongoing functional analysis of the yeast genome. Using a novel transposon-tagging approach, we have analyzed disruption phenotypes, gene expression, and protein localization on a genome-wide scale in Saccharomyces. The data generated from this study may be accessed through our database, TRIPLES ; additionally, all reagents generated in this study are freely available from on-line order forms (linked to TRIPLES as well). multipurpose, mini-transposon, mutant alleles, phenotypes, protein localization, gene expression, Saccharomyces cerevisiae, Web-accessible database, transposon-mutagenized yeast strains, downloaded, tab-delimited, text file, protein localization data, fluorescent micrographs, staining patterns, indirect immunofluorescence analysis of indicated epitope-tagged proteins, subcellular localization of the yeast proteome, visual library, Nucleic Acid Sequence Data Library (GenBank), clone report, graphic map, transposon insertions (represented as flags)

Proper citation: TRIPLES- a database of TRansposon-Insertion Phenotypes Localization and Expression in Saccharomyces (RRID:SCR_005714) Copy   

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http://igdb.nsclc.ibms.sinica.edu.tw/

IGDB.NSCLC database is aiming to facilitate and prioritize identified lung cancer genes and microRNAs for pathological and mechanistic studies of lung tumorigenesis and for developing new strategies for clinical interventions. We integrated and curated various lung cancer genomic datasets to present # lung cancer genes with somatic mutations, experimental supports and statistic significance in association with clinicopathological features; # genomic alterations with copy number alterations (CNA) detected by high density SNP arrays, gain or loss regions detected by arrayed comparative genome hybridization (aCGH), and loss of heterozygosity (LOH) detected by microsatellite markers; # aberrant expression of genes and microRNAs detected by various microarrays. IGDB.NSCLC database provides user friendly interfaces and searching functions to display multiple layers of evidence for detecting lung cancer target genes and microRNAs, especially emphasizing on concordant alterations: # genes with altered expression located in the CNA regions; # microRNAs with altered expression located in the CNA regions; # somatic mutation genes located in the CNA regions; and # genes associated with clinicopathological features located in the CNA regions. These concordant altered genes and miRNAs should be prioritized for further basic and clinical studies.

Proper citation: IGDB.NSCLC (RRID:SCR_006048) Copy   

•   Source: SciCrunch Registry

http://humanmetabolism.org/

A comprehensive biochemical knowledge-base on human metabolism, this community-driven, consensus metabolic reconstruction integrates metabolic information from five different resources: * Recon 1, a global human metabolic reconstruction (Duarte et al, PNAS, 104(6), 1777-1782, 2007) * EHMN, Edinburgh Human Metabolic Network (Hao et al., BMC Bioinformatics 11, 393, 2010) * HepatoNet1, a liver metabolic reconstruction (Gille et al., Molecular Systems Biology 6, 411, 2010), * Ac/FAO module, an acylcarnitine/fatty acid oxidation module (Sahoo et al., Molecular bioSystems 8, 2545-2558, 2012), * a human small intestinal enterocytes reconstruction (Sahoo and Thiele, submitted). Additionally, more than 370 transport and exchange reactions were added, based on a literature review. Recon 2 is fully semantically annotated (Le Nov��re, N. et al. Nat Biotechnol 23, 1509-1515, 2005) with references to persistent and publicly available chemical and gene databases, unambiguously identifying its components and increasing its applicability for third-party users. Here you can explore the content of the reconstruction by searching/browsing metabolites and reactions. Recon 2 predictive model is available in the Systems Biology Markup Language format.

Proper citation: Recon x (RRID:SCR_006345) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org

International database for laboratory mouse. Data offered by The Jackson Laboratory includes information on integrated genetic, genomic, and biological data. MGI creates and maintains integrated representation of mouse genetic, genomic, expression, and phenotype data and develops reference data set and consensus data views, synthesizes comparative genomic data between mouse and other mammals, maintains set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides technical support for database users. Projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI.

Proper citation: Mouse Genome Informatics (MGI) (RRID:SCR_006460) Copy   

•   Source: SciCrunch Registry

http://www.snpedia.com/index.php/SNPedia

Wiki investigating human genetics including information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA. It is based on a wiki model in order to foster communication about genetic variation and to allow interested community members to help it evolve to become ever more relevant. As the cost of genotyping (and especially of fully determining your own genomic sequence) continues to drop, we''''ll all want to know more - a lot more - about the meaning of these DNA variations and SNPedia will be here to help. SNPedia has been launched to help realize the potential of the Human Genome Project to connect to our daily lives and well-being. For more information see the Wikipedia page, http://en.wikipedia.org/wiki/SNPedia * Download URL: http://www.SNPedia.com/index.php/Bulk * Web Service URL: http://bots.SNPedia.com/api.php

Proper citation: SNPedia (RRID:SCR_006125) Copy   

•   Source: SciCrunch Registry

http://proportal.mit.edu/

ProPortal is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data across multiple scales of biological organization--from the genome to the ecosystem--embracing the full diversity of ecotypic variation within this microbial taxon, its sister group, Synechococcus and phage that infect them. The site currently contains the genomes of 13 Prochlorococcus strains, 11 Synechococcus strains and 28 cyanophage strains that infect one or both groups. Cyanobacterial and cyanophage genes are clustered into orthologous groups that can be accessed by keyword search or through a genome browser. Users can also identify orthologous gene clusters shared by cyanobacterial and cyanophage genomes. Gene expression data for Prochlorococcus ecotypes MED4 and MIT9313 allow users to identify genes that are up or downregulated in response to environmental stressors. In addition, the transcriptome in synchronized cells grown on a 24-h light-dark cycle reveals the choreography of gene expression in cells in a ''natural'' state. Metagenomic sequences from the Global Ocean Survey from Prochlorococcus, Synechococcus and phage genomes are archived so users can examine the differences between populations from diverse habitats. Finally, an example of cyanobacterial population data from the field is included.

Proper citation: ProPortal (RRID:SCR_006112) Copy   

•   Source: SciCrunch Registry

http://research.nhgri.nih.gov/CGD/

Manually curated database of all conditions with known genetic causes, focusing on medically significant genetic data with available interventions. Includes gene symbol, conditions, allelic conditions, inheritance, age in which interventions are indicated, clinical categorization, and general description of interventions/rationale. Contents are intended to describe types of interventions that might be considered. Includes only single gene alterations and does not include genetic associations or susceptibility factors related to more complex diseases.

Proper citation: Clinical Genomic Database (RRID:SCR_006427) Copy   

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https://www.ncbi.nlm.nih.gov/geo/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022.

Proper citation: NCBI Epigenomics (RRID:SCR_006151) Copy   

•   Source: SciCrunch Registry

http://mrna.otago.ac.nz/

Database that provides access to mRNA sequences and associated regulatory elements that were processed from Genbank. These mRNA sequences include complete genomes, which are divided into 5-prime UTRs, 3-prime UTRs, initiation sequences, termination regions and full CDS sequences. This data can be searched for a range of properties including specific mRNA sequences, mRNA motifs, codon usage, RSCU values, information content, etc.

Proper citation: Transterm (RRID:SCR_008244) Copy   

•   Source: SciCrunch Registry

http://www.primervfx.com/#welcome

PrimerParadise is an online PCR primer database for genomics studies. The database contains predesigned PCR primers for amplification of exons, genes and SNPs of almost all sequenced genomes. Primers can be used for genome-wide projects (resequencing, mutation analysis, SNP detection etc). The primers for eukaryotic genomes have been tested with e-PCR to make sure that no alternative products will be generated. Also, all eukaryotic primers have been filtered to exclude primers that bind excessively throughout the genome. Genes are amplified as amplicons. Amplicons are defined as only one genes exons containing maximaly 3000 bp long dna segments. If gene is longer than 3000 bp then it is split into the segments at length 3000 bp. So for example gene at length 5000 bp is split into two segment and for both segments there were designed a separate primerpair. If genes exons length is over 3000 bp then it is split into amplicons as well. Every SNP has one primerpair. In addition of considering repetitive sequences and mono-dinucleotide repeats, we avoid designing primers to genome regions which contain other SNPs. -There are two ways to search for primers: you can use features IDs ( for SNP primers Reference ID, for gene/exon primers different IDs (Ensembl gene IDs, HUGO IDs for human genes, LocusLink IDs, RefSeq IDs, MIM IDs, NCBI gene names, SWISSPROT IDs for bacterial genes, VEGA gene IDs for human and mouse, Sanger S.pombe systematic gene names and common gene names, S.cerevisiae GeneBanks Locus, AccNo, GI IDs and common gene names) -you can use genome regions (chromosome coordinates, chromosome bands if exists) -Currently we provide 3 primers collections: proPCR for prokaryotic organisms genes primers -euPCR for eukaryotic organisms genes/exons primers -snpPCR for eukaryotic organisms SNP primers Sponsors: PrimerStudio is funded by the University of Tartu.

Proper citation: PrimerStudio (RRID:SCR_008232) Copy   

•   Source: SciCrunch Registry

http://www.thearkdb.org/arkdb/

This website contains the mapping sequence of poultry. The ArkDB database system aims to provide a comprehensive public repository for genome mapping data from farmed and other animal species. In doing so, it aims to provide a route in to genomic and other sequence from the initial viewpoint of linkage mapping, RH mapping, physical mapping or - possibly more importantly - QTL mapping data. It's supported, in part, by the USDA-CSREES National Animal Genome Research Program in order to serve the poultry genome mapping community. This system represents a complete rewrite of the original version with the code migrated to java and the underlying database targeted at postgres (although any standards-compliant database engine should suffice). The initial release records details of maps and the markers that they contain. There are alternative entry points that target either a chromosome or a specific mapping analysis as the starting point. Limited relationships between markers are recorded and displayed. As with the previous version, all maps are drawn using data extracted from the database on the fly.

Proper citation: ChickBase (RRID:SCR_008147) Copy   

•   Source: SciCrunch Registry

http://microbialgenomics.energy.gov/index.shtml

Through its Microbial Genome Program (MGP) and its Genomics:GTL (GTL) program, DOEs Office of Biological and Environmental Research (BER) has sequenced more than 485 microbial genomes and 30 microbial communities having specialized biological capabilities. Identifying these genes will help investigators discern how gene activities in whole living systems are orchestrated to solve myriad life challenges. The MGP was begun in 1994 as a spinoff from the Human Genome Program. The goal of the program was to sequence the genomes of a number of nonpathogenic microbes that would be useful in solving DOE''s mission challenges in environmental-waste cleanup, energy production, carbon cycling, and biotechnology. Past projects include microbial genome program, microbial cell project, and the Laboratory Science Program at the DOE Joint Genome Institute. The two ongoing projects are Genomics: GTL program and Community Sequencing Program at the DOE Joint Genome Institute. Sponsors: Site sponsored by the U.S. Department of Energy Office of Science, Office of Biological and Environmental Research, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Microbial Genomics Program (RRID:SCR_008140) Copy   

•   Source: SciCrunch Registry

http://mips.helmholtz-muenchen.de/genre/proj/mpcdb/

A database of manually annotated mammalian protein complexes. To obtain a high-quality dataset, information was extracted from individual experiments described in the scientific literature. Data from high-throughput experiments was not included.

Proper citation: Mammalian Protein Complex Data Base (RRID:SCR_008209) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/Projects/C_elegans/index.shtml

The Sanger Institute and the Genome Sequencing Center at the Washington University School of Medicine, St. Louis have collaborated to sequence the genomes of both C. elegans and C. briggsae. The completed C. elegans genome sequence is represented by over 3,000 individual clone sequences which can be accessed through this site (or through WormBase). These sequences are submitted to EMBL whenever the sequence or annotation changes (e.g. modification to gene structures) and these submissions are then mirrored to GenBank and DDBJ. These sequences (along with ESTs and proteins) can be searched on our C. elegans BLAST server. WormBase is the repository of mapping, sequencing and phenotypic information for C. elegans. The worm informatics group at the Sanger Institute play a key role in assembling the whole database. They also curate and develop some of the constituent databases that comprise WormBase.

Proper citation: Caenorhabditis Genome Sequencing Projects (RRID:SCR_008155) Copy   

•   Source: SciCrunch Registry