Featured Articles:
State of cat genomics.
Stephen J. O’Brien, Warren Johnson, Carlos
Driscoll, Joan Pontius, Jill Pecon-Slattery, and Marilyn Menotti-Raymond
TRENDS IN GENETICS 24(6): 268-279, June 2008
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding
sequences
Tarjei S. Mikkelsen, Broad Institute
of Harvard and MIT; Matthew Breen & Shannon Duke, North Carolina State
University; et al. (NCSU)
NATURE 447:167-177,
May 10, 2007
Vertebrates
general resources | fish & amphibians | companion
animals: cat & dog |
farm animals: chicken | cow | pig | sheep
model
vertebrates: mouse | rat |
Xenopus and zebrafish (on Model
Organisms page)
General Resources
ARKdb (Roslin Institute, Scotland)
http://www.thearkdb.org/
ARKdb is a public repository for genome data from farmed and other animal
species. The data is manually annotated and includes information about loci
and markers, literature citations, genetic and cytogenetic map assignments,
and experimental techniques. Data is available for 10 species: cat,
chicken, cow, deer, horse, pig, salmon, sheep, tilapia, and turkey (see
links at http://www.thearkdb.org/species.html).
Ensembl (EMBL-EBI and the Sanger Institute)
http://www.ensembl.org/
Ensembl is a system providing automated genome annotation and graphic displays
of annotated genomes. Gene predictions are based on experimental evidence obtained
from several sites, including UniProt/Swiss-Prot, NCBI RefSeq, and UniProt/TrEMBL.
Vertebrate genomes available include: Pan troglodytes, Macaca mulatta,
Canis familiaris, Bos Taurus, Monodelphis domestica, Gallus gallus, Takifugu
rubripes, Tetraodon nigroviridis, and several model species genomes.
Entrez Genome Project (NCBI)
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj
This database is a searchable collection of complete and in-progress genome
sequencing, assembly, annotation, and mapping projects for cellular organisms.
The database contains organism-specific overviews that also provide access
to the projects in the database. Only projects that have submitted data to
NCBI, intend to submit data, or have received public funding are included in
this database. [Note: enter the organism name in the search
box]
TIGR Gene Indexes (animals)
http://www.tigr.org/tdb/tgi/index.shtml
TIGR Gene Indexes are built using EST sequences extracted from dbEST and other
sources, screened for quality control, and clustered together. Clusters are
assembled into Tentative Consensus (TC) sequences. TCs are then annotated based
on searches against a non-redundant protein database. The TIGR website hosts
gene indexes for close to 20 vertebrates including: dog, cattle, chicken, Xenopus
laevis, Xenopus tropicalis, and nine fish species (salmon, catfish, fugu,
trout, and others).
UCSC Genome Bioinformatics (Center for Biomolecular Science and Engineering,
UC Santa Cruz)
http://genome.cse.ucsc.edu/
The
UCSC Genome Bioinformatics group provides access to genomic sequence data and
prepares draft assemblies and annotations for a large collection of genomes.
Several tools are available for viewing data from the level of a chromosome map
to sequence details. Multiple types of annotations are provided, including known
and predicted genes, ESTs, mRNAs, chromosomal bands, mouse homologies, and more.
Links to major repositories and resources are also included. Genome data are
available for 13 vertebrates: human, chimpanzee, rhesus, dog,
cow, mouse, rat, opossum, chicken, X. tropicalis, zebrafish, fugu,
and tetraodon.
Vertebrate Genome Annotation (VEGA, Sanger
Institute)
http://vega.sanger.ac.uk/index.html
VEGA
is a central repository for selected regions (e.g., chromosomes or gene function)
of vertebrate genome sequences that are manually annotated and updated frequently.
Links to other relevant resources and sequence data are provided. The species
included are: human, mouse, zebrafish, pig, and dog.
Online Mendelian Inheritance in Animals (OMIA)
http://www.ncbi.nlm.nih.gov/sites/entrez?db=omia
While not a genome resource, OMIA provides textual information about genes, inherited disorders and traits in animal species (other than human and mouse) and links to relevant records from other databases. NCBI maintains a mirror site for the original OMIA hosted by the Australian National Genomic Information Service.
Fish & Amphibians
Zebrafish and Xenopus links are
on the Model
Organisms page.
Salmonids Genomics (Aquaculture Genome Projects, National
Animal Genome Research Program, USDA )
http://www.animalgenome.org/aquaculture/salmonids/
NAGRP serves as a central information center for livestock and aquaculture
genome projects. This page on salmonids includes links to articles, physical
and genetic maps, ESTs and microarrays, QTL, and other resources. Atlantic
salmon and rainbow trout are the best characterized species in terms of genomics,
although genetic maps have been developed for other species such as Chinook
salmon and Artic char.
Companion Animals
Cat Genome Project (Laboratory of Genetic Diversity, National Cancer
Institute)
http://home.ncifcrf.gov/ccr/lgd/comparative_genome/catgenome/index_n.asp
Cat
genetic maps, information about the cat as a model for several human diseases,
literature, and links.
Cat Genome Resources (NCBI)
http://www.ncbi.nlm.nih.gov/projects/genome/guide/cat/
A summary of resources related to cat genome and biology. Includes direct links to NCBI radiation hybrid and genetic linkage maps, sequence, and taxonomy data and to other sequencing projects
and web sites.
Canine Genome Resources (NCBI)
http://www.ncbi.nlm.nih.gov/genome/guide/dog/
A summary of resources related to dog genome and biology. Includes direct
links to NCBI map, sequence, and taxonomy data and to other dog sequencing
projects and web sites.
Cytogenetics and Cancer at NCSU
http://www2.ncsu.edu/unity/lockers/project/cvmaprhome/breen_matthew.htm
Research
activities in Dr. Matthew Breen’s lab focus on the cellular
genomics of canine cancers and the investigation of any related genetic etiology
shared with humans.
One product of the rsearch in this lab is a 4249 marker
FISH/RH map of the canine genome: http://www.cvm.ncsu.edu/mbs/breen/dog_map.htm
Dog (Canis familiaris) Genome Browser Gateway (UCSC))
http://genome.ucsc.edu/cgi-bin/hgGateway?clade=vertebrate&org=Dog&db=0&hgsid=73953940
The full sequence of the canine genome accessible through the Genome Browser
and other tools available at the UCSC Bioinformatics web site.
Farm Animals
Note: Ensembl (described
above) has genome information for several farm animals, including:
Horse--newly released.
Also cow, rabbit, and chicken.
U.S. Livestock Species Genome Projects (National
Animal Genome Research Program, USDA)
http://www.animalgenome.org/
This site serves as an information center for livestock genome projects, currently
hosting data for sheep, horse, cattle, chicken, and swine projects. Each project
has a web page that serves as a central resource for access to upcoming meetings,
databases, maps, resources, and links. Links to the project pages:
Cattle: http://www.animalgenome.org/cattle/
Chicken: http://poultry.mph.msu.edu/
Horse: http://www.uky.edu/Ag/Horsemap/
Sheep:http://iowa.thearkdb.org/browser?species=sheep
Swine: http://www.animalgenome.org/pigs/
Chicken Genome Resources (NCBI)
http://www.ncbi.nlm.nih.gov/genome/guide/chicken/
A summary of resources related to chicken genome and biology. Includes direct
links to NCBI map, sequence, and taxonomy data and to other chicken sequencing
projects and web sites.
Chicken Variation Database (ChickVD; Beijing Genomics
Institute, Chinese Academy of Sciences)
http://chicken.genomics.org.cn/index.jsp
ChickVD
hosts sequence variation data, variation analysis in the context of chicken genes,
cDNAs, chicken orthologs of human disease genes, genetic markers, and quantitative
trait loci (QTLs).
Bovine Genome Resources (NCBI)
http://www.ncbi.nlm.nih.gov/genome/guide/cow/
A summary of resources related to bovine genome and biology. Includes direct
links to NCBI map, sequence, and taxonomy data and to other sequencing projects
and web sites.
Pig Genome Resources (NCBI)
http://www.ncbi.nlm.nih.gov/genome/guide/pig/
A summary of resources related to pig genome and biology. Includes direct
links to NCBI map, sequence, and taxonomy data and to other sequencing projects
and web sites.
The Swine Genome Sequencing Consortium--News and Updates
http://www.animalgenome.org/pigs/genomesequence/
WebChrom: porcine physical map
http://www.sanger.ac.uk/Projects/S_scrofa/WebFPC/WebChrom/index.shtml
Sheep Genome Resources (NCBI)
http://www.ncbi.nlm.nih.gov/genome/guide/sheep/
A summary of resources related to sheep genome and biology. Includes direct
links to NCBI map, sequence, and taxonomy data and to other sequencing projects
and web sites.
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