BEAP: The BLAST Extension and Alignment Program- a tool for contig construction and analysis of preliminary genome sequence.

ABSTRACT:

Background

Fine-mapping projects require a high density of SNP markers and positional candidate gene sequences. In species with incomplete genomic sequence, the DNA sequences needed to generate markers for fine-mapping within a linkage analysis confidence interval may be available but may not have been assembled. To manually piece these sequences together is laborious and costly. Moreover, annotation and assembly of short, incomplete DNA sequences is time consuming and not always straightforward.

Findings

We have created a tool called BEAP that combines BLAST and CAP3 to retrieve sequences and construct contigs for localized genomic regions in species with unfinished sequence drafts. The rational is that a completed genome can be used as a template to query target genomic se

SUBMITTER: Koltes JE 

PROVIDER: S-EPMC2642851 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature