A Survey of Canine Expressed Sequence Tags and a Display of Their Annotations Through a Flexible Web-Based Interface

Palmer, L. E., O'Shaughnessy, A. L., Preston, R. R., Santos, L., Balija, V. S., Nascimento, L. U., Zutavern, T. L., Henthorn, P. S., Hannon, G. J., McCombie, W. R. (2003) A Survey of Canine Expressed Sequence Tags and a Display of Their Annotations Through a Flexible Web-Based Interface. Journal of Heredity, 94 (1). pp. 15-22. ISSN 00221503 (ISSN)

URL: http://www.ncbi.nlm.nih.gov/pubmed/12692157
DOI: 10.1093/jhered/esg003

Abstract

We have initially sequenced approximately 8,000 canine expressed sequence tags (ESTs) from several complementary DNA (cDNA) libraries: testes, whole brain, and Madin-Darby canine kidney (MDCK) cells. Analysis of these sequences shows that they provide partial sequence information for about 5%-10% of the canine genes. An analysis pipeline has been created to cluster the ESTs and to map individual ESTs as well as clustered ESTs to both the human genome and the human proteome. Gene ontology (GO) terms have been assigned to the ESTs and clusters based on their top matches to the International Protein Index (IPI) set of human proteins. The data generated is stored in a MySQL relational database for analysis and display. A Web-based Perl script has been written to display the analyzed data to the scientific community.

Item Type: Paper
Uncontrolled Keywords: brain cell line conference paper data base DNA library dog expressed sequence tag gene gene cluster gene ontology genome international protein index data base Internet nucleotide sequence ontogeny pedigree phenotypic variation priority journal proteomics sequence analysis testis Animals Base Sequence Databases, Genetic Dogs Expressed Sequence Tags Molecular Sequence Data Canis familiaris Mammalia
Subjects: bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > analysis and processing > Sequence Data Processing
CSHL Authors:
Communities: CSHL labs > Hannon lab
CSHL labs > McCombie lab
Depositing User: Matt Covey
Date Deposited: 09 Jan 2013 16:51
Last Modified: 09 Jan 2013 16:51
Related URLs:
URI: http://repository.cshl.edu/id/eprint/26456

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