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Animal Genome Database

Database of comparative gene mapping between species to assist the mapping of the genes related to phenotypic traits in livestock. The linkage maps, cytogenetic maps, polymerase chain reaction primers of pig, cattle, mouse and human, and their references have been included in the database, and the correspondence among species have been stipulated in the database. AGP is an animal genome database developed on a Unix workstation and maintained by a relational database management system. It is a joint project of National Institute of Agrobiological Sciences (NIAS) and Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF-Institute), under cooperation with other related research institutes. AGP also contains the Pig Expression Data Explorer (PEDE), a database of porcine EST collections derived from full-length cDNA libraries and full-length sequences of the cDNA clones picked from the EST collection. The EST sequences have been clustered and assembled, and their similarity to sequences in RefSeq, and UniGene determined. The PEDE database system was constructed to store sequences and similarity data of swine full-length cDNA libraries and to make them available to users. It provides interfaces for keyword and ID searches of BLAST results and enables users to obtain sequence data and names of clones of interest. Putative SNPs in EST assemblies have been classified according to breed specificity and their effect on coding amino acids, and the assemblies are equipped with an SNP search interface. The database contains porcine nucleotide sequences and cDNA clones that are ready for analyses such as expression in mammalian cells, because of their high likelihood of containing full-length CDS. PEDE will be useful for researchers who want to explore genes that may be responsible for traits such as disease susceptibility. The database also offers information regarding major and minor porcine-specific antigens, which might be investigated in regard to the use of pigs as models in various medical research applications.

URL: http://animal.dna.affrc.go.jp/agp/index.html

Resource ID: nif-0000-21029     Resource Type: Resource     Version: Latest Version

Keywords

est, expression, gene, amino acid, animal, antigen, breed, cattle, cdna, cell, chain, clone, coding, cytogenetic, genome, human, linkage, livestock, mammalian, map, mouse, nucleotide, organism, phenotypic, pig, polymerase, porcine, primer, reaction, sequence, snp, specie, swine, trait

Synonyms

AGP

Additional Resource Types

database

Supercategory

Resource

Parent Organization

Original Submitter

Anonymous

Version Status

Curated

Submitted On

12:00am September 8, 2010

Originated From

SciCrunch

Changes from Previous Version

First Version

Version 1

Created 5 years ago by Anonymous