This website uses cookies in order to improve our services. If you proceed visiting this website you accept the usage of cookies. For more info please read our Data Privacy statement.

 

Animal Genetic Databases


General Genetics Databases Animal Genetics | Cancer Genetics | Human Genetics | Microbial Genetics | Plant & Fungi Genetics | RNA Databases


 

Aniseed

This morphological simplicity is paralleled by the simplicity of the Ciona intestinalis genome, which has been sequenced and assembled (Joint Genome Institute, USA and Kyoto university, Japan, http://genome.jgi-psf.org/Cioin2/Cioin2.home.html). This genome is similar in size and gene density to Drosophila and C. elegans and most genes present in 2-4 copies in the vertebrate genomes have a single Ciona orthologue (Dehal et al., 2002). The genome of a second species, Ciona savignyi, has recently been released by the MIT (http://www.broadinstitute.org/annotation/ciona/), opening the way to cross species comparisons. This genomic effort has been complemented by several large-scale in situ hybridisation (ISH) screens. These screens have provided a wealth of molecular markers or effectors for the different embryonic tissues.

Website

Ant genomics database

You can Blast search ant genomes and download genome FASTA files.

Source: Queen Mary University of London

ArkDB

The ArkDB database system aims to provide a comprehensive public repository for genome mapping data from farmed and other animal Species. In doing so, we aim 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.

ArkDB 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 (via the Species table or Maps menu respectively). Limited relationships between markers are recorded and displayed.

Source: The Roslin Institute

BeetleBase

BeetleBase is a comprehensive sequence database and important community resource for Tribolium genetics, genomics and developmental biology. Beetlebase contains genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The current version of Beetlebase is built on the Tribolium castaneum 3.0 Assembly (Tcas 3.0) released by the Human Genome Sequencing Center at the Baylor College of Medicine.

Source: K-State Bioinformatics Center

BirdBase

The sequencing of several bird genomes and the anticipated sequencing of many more provided the impetus to develop a model organism database devoted to the taxonomic class: Aves. Birds provide model organisms important to the study of neurobiology, immunology, genetics, development, oncology, virology, cardiovascular biology, evolution and a variety of other life sciences. Many bird species are also important to agriculture, providing an enormous worldwide food source worldwide. Genomic approaches are proving invaluable to studying traits that affect meat yield, disease resistance, behavior, and bone development along with many other factors affecting productivity. In this context, BirdBase will serve both biomedical and agricultural researchers.

Website

Echinobase

Echinobase aims to provide a comparative genomics platform for the echinoderm clade.
Currently, genomes for Strongylocentrotus purpuratus, Lytechinus variegatus, Patiria miniata, Parastichopus parvamensis and Ophiothrix spiculata are posted here.
Transcriptomes for these and other echinoderms are also presented.
We continue to expand our information system as additional genome and transcriptome assemblies become available.

Source: Echinobase

EMAGE

EMAGE is a database of in situ gene expression data in the mouse embryo and an accompanying suite of tools to search and analyse the data.

mRNA in situ hybridisation, protein immunohistochemistry, in situ transgenic reporter data, and in situ enhancer data is included. These are sourced from the community and our curators take this data and describe it in a standardised way that allows data query and exchange. The description includes a text-based component but the unique aspect of EMAGE is its spatial annotation focus.

Source: EMAGE

Feline Genome Project

The Feline Genome Project is an international research effort focused on the improvement of genomic and genetic resources for the domestic cat. The project includes research efforts from scientists from around the world and is inclusive of all efforts. The National Institutes of Health have provided the majority of the support for large-scale sequencing centers, such as the Broad Institute and The Genome Institute of Washington University at St. Louis to develop the DNA sequence of the cat genome. These large efforts are supported by researchers who have continued and long term interests in developing the cat as a model for human disease and improving health of the domestic cat. Public groups, such as Hill’s Pet Food, Inc., have also contributed to the sequencing of the cat.

Source: University of Missouri

FlyBase

A Database of Drosophila Genes & Genomes

Source: FlyBase

Fugu genome project

The fugu (Fugu rubripes) genome project was initiated in 1989 by Sydney Brenner and his colleagues Greg Elgar, Sam Aparicio and Byrappa Venkatesh. In 1993, this team showed that the fugu genome is only 390 Mb, about one-eighth the size of the human genome, yet it contains a similar repertoire of genes to humans (Brenner et al., Nature 366:265-268, 1993). Therefore, fugu was proposed as a useful model for annotating the human genome. This, in fact, ushered in the era of comparative genomics. Fugu genome is among the smallest vertebrate genomes and has proved to be a useful ‘reference’ genome for identifying genes and other functional elements such as regulatory elements in human and other vertebrate genomes, and for understanding the structure and evolution of vertebrate genomes. A ‘draft’ sequence of the fugu genome was determined by the International Fugu Genome Consortium in 2002 using the 'whole-genome shotgun' sequencing strategy. The results of the assembly (v2) are reported in Science 297:1301-1310 (2002). Fugu is the second vertebrate genome to be sequenced, the first being the human genome.

Source: Institute of Molecular and Cell Biology, A*STAR, Singapore

Horse Genome Project

The Horse Genome Project is a cooperative international effort by over 100 scientists in 20 countries to define the genome, the DNA sequence, of the domestic horse. With this knowledge, scientists can begin to understand the genetic aspects of equine physiology and disease. Genetic tools have the potential to help researchers find new therapies and treatments for diseases such as laminitis, respiratory diseases, etc.

Source: Horse Genome Project

Hymenoptera Genome Database

The Hymenoptera Genome Database (HGD) is an informatics resource supporting genomics of insect species of this order. HGD provides access to the genomes of bees Apis mellifera, Bombus terrestris and B. impatiens, the parasitoid wasp Nasonia vitripennis, and seven species of ants available through the Ant Genomes Portal. It will soon incorporate genome databases for two additional species of bees, Apis dorsata and A. florea, as well as two additional species of ants. Combining these species into a single resource allows biologists to leverage the genome information, and enhances the value of genomic data for each species by facilitating cross-species comparisons.

Source: Hymenoptera Genome Database

Lizardbase

A growing interest in lizard biology is generating an unprecedented amount of novel data. With newly sequenced genomic assemblies, expression profiles, ecological data, and population-specific morphological data, lizards are fast becoming important biological models from functional ecology to medical genetics. However, in this era of high-throughput biology, we now face one of its greatest challenges: the management and integration of different types of data.

lizardbase is being developed to fill the need for a centralized and consolidated informatics resource that can connect many active areas of lizard research. Our primary goal is to provide biologists with a forum to facilitate both scientific discovery and collaboration. Furthermore, we are building this site to facilitate citizen involvement in the sciences.

Source: Lizardbase

MGI - Mouse Genome Informatics

MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.

Website

NAGRP Pig Genome Coordination Program

The U.S. Pig Genome Project

Website

National Animal Genome Research Program

This is the USDA NRSP-8 Program (National Animal Genome Research Program, NAGRP) Bioinformatics Coordination Project web site. The project is supported by funding from the USDA-NRI (former CSREES) for the periods 2003-2008 and 2008-2013.
This site is designed as an information center to serve the national animal genome research projects of cattle, chicken, pigs, sheep, horse, and aquaculture species. This is home to databases and web sites (being) built for structural, functional and application oriented studies of the animal genomics, to serve the purpose of research, education and related activities in the scientific, industrial and educational communities in the states and world wide.

Source: National Animal Genome Research Program

Planform

PlanformDB is an experiment-phenotype database of planarian regeneration data published in the literature. Currently, it contains more than 1,000 different experiments, and we are continuously expanding it with new results. PlanformDB can be accessed with the software tool Planform, which facilitates the search, mining, and modification of the dataset.

Source: Lobo Lab

Rat Genome Database (RGD)

The Rat Genome Database (RGD) was established in 1999 and is the premier site for genetic, genomic, phenotype, and disease data generated from rat research. In addition, it provides easy access to corresponding human and mouse data for cross-species comparisons. RGD's comprehensive data and innovative software tools make it a valuable resource for researchers worldwide.

Website

The Animal Genome Size Database

The Animal Genome Size Database, Release 2.0, is a comprehensive catalogue of animal genome size data. Haploid DNA contents (C-values, in picograms) are currently available for 5635 species (3731 vertebrates and 1904 non-vertebrates) based on 7286 records from 683 published sources.
Source: Animal Genome Size Database

Website

TreeFam - database of animal gene trees

TreeFam is a database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.

Source: EMBL-EBI

WormBase

WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes. Founded in 2000, the WormBase Consortium is led by Paul Sternberg of CalTech, Paul Kersey of the EBI, Matt Berriman of the Wellcome Trust Sanger Institute, and Lincoln Stein of the Ontario Institute for Cancer Research.

Website

Xenbase

Xenbase's mission is to provide the international research community with a comprehensive, integrated and easy to use web based resource that gives access the diverse and rich genomic, expression and functional data available from Xenopus research. Xenbase also provides a critical data sharing infrastructure for many other NIH-funded projects, and is a focal point for the Xenopus community. In addition to our primary goal of supporting Xenopus researchers, Xenbase enhances the availability and visibility of Xenopus data to the broader biomedical research community.

Source: Xenbase

ZFIN - Zebrafish Model Organism Database

ZFIN serves as the zebrafish model organism database. The long term goals for ZFIN are a) to be the community database resource for the laboratory use of zebrafish, b) to develop and support integrated zebrafish genetic, genomic and developmental information, c) to maintain the definitive reference data sets of zebrafish research information, d) to link this information extensively to corresponding data in other model organism and human databases, e) to facilitate the use of zebrafish as a model for human biology and f) to serve the needs of the research community.

Source: University of Oregon


Pin It