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Genetic & Genomic Resources for Model Organisms

Many NIGMS-funded investigators and other scientists use model organisms in their research, and to facilitate their work, the Institute has supported the development of a number of major model organism resources. These resources and more are listed below, and we welcome your suggestions for revisions to this page, including resources for additional organisms or new resources for organisms that are already listed.

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Arabidopsis thaliana  

Arabidopsis thaliana
NIGMS Contact: Michael Reddy, Ph.D., reddymk@nigms.nih.gov, 301-594-0943

 

The Arabidopsis Information Resource (TAIR) Link to external Web site  
TAIR provides a comprehensive resource for the Arabidopsis thaliana scientific community. TAIR hosts a searchable, relational database.

The Arabidopsis Gene Expression Database (AREX) Link to external Web site
AREX curates published Arabidopsis gene expression information and combines it with new data gained from traditional and microarray studies, so that all expression data can be found in a single, searchable database.

Caenorhabditis elegans   Caenorhabditis elegans
NIGMS Contact: Daniel Janes, Ph.D., janesde@mail.nih.gov, 301-594-0943

 

Trans-NIH C. elegans Initiative 
This site lists several links to funding opportunities, C. elegans repositories, microarray resources, and C. elegans Web sites.  

Chlamydomonas   Chlamydomonas
NIGMS Contact: Anthony D. Carter, Ph.D., cartera@nigms.nih.gov, 301-594-0943

 

Chlamydomonas Resource Center Link to external Web site 
This site contains link to tools, resources, and other information for the Chlamydomonas scientific community.

Chlamydomonas Genome Project Link to external Web site 
This site contains sequence and annotation information produced by the Chlamydomonas reinhardtii genome project.

Ciona intestinalis   Ciona
NIGMS Contact: Susan Haynes, Ph.D., hayness@nigms.nih.gov, 301-594-0943

 

Ciona intestinalis Genome Project Link to external Web site 
This site provides information and links to genomic resources for the Ciona scientific community. 

Ciona savignyi Reference Genome and Genetic Map Link to external Web site
This site has downloadable data files from studies to integrate the C. savignyi reference sequence with a comprehensive genetic map. Genome comparisons between C. savignyi and C. intestinalis are also available.

Ascidian Stock Center Link to external Web site
The Ascidian Stock Center provides wild type C. intestinalis and C. savignyi strains to the research community. Some stable transgenic strains are also available.

Ensembl Annotations

Ensembl is a software for producing and maintaining automatic annotation on selected eukaryotic genomes.

Ensembl-Annotated Ciona intestinalis genome Link to external Web site

Ensembl-Annotated Ciona savignyi genome Link to external Web site

Daphnia Pulex   Daphnia pulex
NIGMS Contact: Anthony D. Carter, Ph.D., cartera@nigms.nih.gov, 301-594-0943.

 

The Daphnia Genomics Consortium Link to external Web site 
The Daphnia Genomics Consortium (DGC) is an international network of investigators committed to advancing the use of the freshwater crustacean, Daphnia, as a model system for studies in ecology, evolution and environmental sciences.

The U.S. Department of Energy Joint Genome Institute Daphnia portal Link to external Web site 
This site provides access to sequence data as well as to a set of tools available for use with Daphnia.

Dictyostelium discoideum   Dictyostelium discoideum
NIGMS Contact: Stefan Maas, Ph.D., maassw@nigms.nih.gov, 301-594-0943.


DictyBase Link to external Web site 
This site provides a single portal for access to Dictyostelium discoideum and related Dictyostelid genome information, curated Dictyostelium literature and access to experimental resources such as the Dicty Stock Center.

The Dicty Stock Center Link to external Web site 
The Dicty Stock Center is a central repository of strains of Dictyostelium discoideum and related organisms. Strains and reagents are distributed free of charge to bona fide teaching and non-profit research institutions.
Dog   Dog 
NIGMS Contact: Irene A. Eckstrand, Ph.D., eckstrai@mail.nih.gov, 301-594-0943

 

NHGRI Dog Genome Project
This site describes a collaborative study involving scientists at the University of California, Berkeley; the University of Oregon; and the Fred Hutchinson Cancer Research Center. It is aimed at producing a map of all the chromosomes in dogs.

Drosophila   Drosophila
NIGMS Contact: Michael Bender, Ph.D., mbender@nigms.nih.gov, 301-594-7549

 

Trans-NIH Fly Initiative 
This site lists several links to funding opportunities, resources, and Web sites for the Drosophila scientific community.

Bloomington Drosophila Stock Center at Indiana University Link to external Web site 
The Bloomington Stock Center collects, maintains, and distributes Drosophila melanogaster strains for research.

Drosophila Genomics Resource Center (DGRC) Link to external Web site 
The DGRC serves the Drosophila research community by manufacturing and distributing microarrays; collecting and distributing DNA vectors, cDNAs, and ESTs; collecting and distributing cell lines; assisting scientists in the use of these materials; and sponsoring and testing emerging genomics technologies on behalf of the Drosophila research community.

Drosophila RNAi Screening Center (DRSC) Link to external Web site 
The DRSC has generated a library of double-stranded RNAs (dsRNAs) directed against all predicted open reading frames, and provides a facility for conducting high-throughput cell-based RNA interference (RNAi) screens to identify genes involved in specific functions.

Escherichia coli   Escherichia coli
NIGMS Contact: Michael Reddy, Ph.D., michael.reddy@nih.gov, 301-594-0943

 

PortEco Link to external Web site
A next-generation resource for knowledge and data about the biology of Escherichia coli K-12 group strains, its bacteriophages, plasmids, and mobile genetic elements. Also featured is EcoliWiki Link to external Web site, a subsystem for community annotation.

EcoCyc Link to external Web site
EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation Link to external Web site of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.

EcoGene Link to external Web site
The EcoGene database contains updated information about the E. coli K-12 genome.  A major EcoGene focus has been the re-evaluation of translation start sites.

RegulonDB Link to external Web site
RegulonDB is a computational model of mechanisms of transcriptional regulation in E. coli K-12. 

Coli Genetics Stock Center Link to external Web site
The Coli Genetics Stock Center at Yale provides samples primarily of strain K-12. The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature.

Apis mellifera   Honey Bee
NIGMS Contact: Michael Sesma, Ph.D., msesma@mail.nih.gov, 301-594-2772
 
This site contains information and resources from the Apis mellifera genome project. The ~200Mbase genome is being sequenced using a combined whole genome shotgun and BAC clone approach.
 
This site contains an expressed sequence tag (EST) resource for the bee brain.
 
This site, hosted by NIH's National Center for Biotechnology Information, contains a tool to use map data to find gene information by position relative to other landmarks in the honey bee genome.
 
The Honey Bee Genome Database, available at this site, contains the Apis mellifera genome assembly version 1.1 released by the Baylor Human Genome Sequencing Center in January 2004.
 
The BeeSpace environment enables users to navigate a uniform space of diverse databases and literature sources for hypothesis development and testing. The software system goes beyond a searchable database, using statistical literature analyses to discover functional relationships between genes and behavior.
 
  Hydra
NIGMS Contact: Susan Haynes, Ph.D., hayness@nigms.nih.gov, 301-594-0943

 

Hydra magnipapillata Genome Browser Link to external Web site 
This site contains genomic resources for the Hydra scientific community and is useful for researchers interested in evolution of metazoans and their genomes. Image credit: Hiroshi Shimizu

Mouse   Mouse
NIGMS Contact: Michelle R.J. Hamlet, Ph.D., hamletm@nigms.nih.gov, 301-594-3900

 

Trans-NIH Mouse Initiative 
This site lists several links to funding opportunities, genetic and genomic resources, and other information for the mouse scientific community.

Mouse Genome Informatics Link to external Web site 
This site, hosted by the Jackson Laboratory, provides integrated access to data on the genetics, genomics, and biology of the mouse. 

The Peromyscus Genetic Stock Center Link to external Web site
This site provides a reliable source of Peromyscus (deer mice) and related materials to the national scientific and educational communities. 

Mouse Phylogeny Viewer Link to external Web site
This online tool provides access to complete genomic data on 162 laboratory mouse strains.

Collaborative Cross Link to external Web site
This site provides information and resources on the Collaborative Cross, a large, genetically diverse panel of inbred mouse strains that are being developed through a community effort.

Neurospora crassa   Neurospora crassa
NIGMS Contact: Michael Bender, Ph.D., mbender@nigms.nih.gov, 301-594-0943

 

Trans-NIH Neurospora Initiative
This NIH-hosted site contains useful information for the Neurospora scientific community including links to genomic resources, annotation and gene descriptions, and culture collections.

Plasmodium   Plasmodium
NIGMS Contact: Irene A. Eckstrand, Ph.D., eckstrai@mail.nih.gov, 301-594-0943

 

PlasmoDB Link to external Web site 
This site contains the database for the malaria parasite genome project and provides access to finished sequence for the Plasmodium falciparum strain 3D7. 

Rattus norvegicus   Rat
NIGMS Contact: Michelle R.J. Hamlet, Ph.D., hamletm@nigms.nih.gov, 301-594-3900

 

NIH Rat Genomics and Genetics Web site 
This Web site serves as a central point for information on NIH-sponsored and related rat genetic and genomic activities and resources.  

Tetrahymena thermophilia   Tetrahymena
NIGMS Contact: Anthony D. Carter, Ph.D., cartera@nigms.nih.gov, 301-594-0943

 

Tetrahymena Genome Database Link to external Web site 
This web site provides an up-to-date source of information for researchers in the Tetrahymena community and investigators interested in other ciliates.

Xenopus Xenopus
NIGMS Contact: Tanya Hoodbhoy, Ph.D., tanyah@mail.nih.gov, 301-594-0943

 

Trans-NIH Xenopus Initiative 
This site tracks NIH�s progress and plans regarding support of the genomic and genetic needs for Xenopus research. It also provides links to community resources and to information about courses, meetings, and publications.

Xenopus Gene Collection (XGC) 
The XGC is an NIH initiative that supports the production of cDNA libraries, clones and 5�/3� sequences to provide a set of full-length (open reading frame) sequences and cDNA clones of expressed genes for Xenopus laevis and Xenopus tropicalis. All resources generated by the XGC are publicly accessible to the biomedical research community.  

Saccharomyces   Yeast
NIGMS Contact: Michael Bender, Ph.D., mbender@nigms.nih.gov, 301-594-0943

 

Saccharomyces Genome Database Link to external Web site 
The Saccharomyces Genome Database (SGD) is a comprehensive, publicly accessible resource about the yeast Saccharomyces cerevisiae (commonly known as baker's or budding yeast). SGD collects and organizes information about the molecular biology and genetics of S. cerevisiae, including review of the published literature, incorporation of DNA sequence updates, and management of S. cerevisiae gene nomenclature.

Yeast Intron Database Link to external Web site 
This site contains information about the spliceosomal introns of S. cerevisiae, including documentation of actual splice site usage under different experimental conditions.

The Schizosaccharomyces pombe Genome Project Link to external Web site 
This site contains links to information, links, and resources for the S. pombe scientific community. 

Zebrafish   Zebrafish
NIGMS Contact: Susan Haynes, Ph.D., hayness@nigms.nih.gov, 301-594-0943

 

Trans-NIH Zebrafish Initiative 
This site is a central information resource for obtaining information about zebrafish genetic and genomic resources, funding opportunities, courses and scientific meetings, and selected reports and publications.

Zebrafish Gene Collection (ZGC) 
The ZGC is an NIH initiative that supports the production of cDNA libraries, clones, and sequences to provide a complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for zebrafish. All resources generated by the ZGC are publicly accessible to the biomedical research community.

Zinc Finger Nuclease Target Site Algorithm Link to external Web site
This resource is used to recover sequences to use for zinc finger nucleases.

This page last reviewed on July 16, 2014