GenomeLKPG: A comprehensive proteome sequencedatabase for taxonomy studies

GenomeLKPG : A comprehensive proteome sequencedatabase for taxonomy studies

Bresel, Anders (author): Linköpings universitet,Biomolekylär och Organisk Elektronik,Tekniska högskolan

Persson, Bengt (author): Linköpings universitet,Bioinformatik,Tekniska högskolan

(creator_code:org_t)

Abstract Subject headings

Background: In order to perform taxonomically unbiased analyses of protein relationships, there is a need ofcomplete proteomes rather than databases with bias towards well characterized protein families. However, nocomprehensive resource of completed proteomes is currently available. Instead, the proteomes need to be down-loaded manually from di®erent servers, all using different filename conventions and fasta header formats. Results: We have developed a semi-automatic algorithm that retrieves complete proteomes from multiple FTP-servers and maps the species-speci¯c sequence entries to the NCBI taxonomy. The compiled data is provided ina sequence database named genomeLKPG. Conclusions: The usefulness of genomeLKPG is proven in several published taxonomical studies.

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