Abstract
BackgroundFine-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.FindingsWe 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 sequence for closing the gaps or extending contig sequence length in species whose genome is incomplete on the basis that good homology exists. Each user must define what template sequence is appropriate based on comparative mapping data such as radiation hybrid (RH) maps or other evidence linking the gene sequence of the template species to the target species.ConclusionThe BEAP software creates contigs suitable for discovery of orthologous genes for positional cloning. The resulting sequence alignments can be viewed graphically with a Java graphical user interface (GUI), allowing users to evaluate contig sequence quality and predict SNPs. We demonstrate the successful use of BEAP to generate genomic template sequence for positional cloning of the Angus dwarfism mutation. The software is available for free online for use on UNIX systems at .
Highlights
MethodsBEAP construction The BLAST and CAP3 processes were linked via Perl scripts to create a sequence assembly pipeline (see Additional file 1 for rationale, Additional File 1 Figure S5 and Additional file 2) BLAST was looped in an iterative process such that after all the queries, each unique sequence was used as template for the round of BLAST against the initial databases
Fine-mapping projects require a high density of SNP markers and positional candidate gene sequences
We demonstrate the successful use of BEAP to generate genomic template sequence for positional cloning of the Angus dwarfism mutation
Summary
BEAP construction The BLAST and CAP3 processes were linked via Perl scripts to create a sequence assembly pipeline (see Additional file 1 for rationale, Additional File 1 Figure S5 and Additional file 2) BLAST was looped in an iterative process such that after all the queries, each unique sequence was used as template for the round of BLAST against the initial databases. The number of BLAST rounds was monitored such that only the desired number of reiterative BLAST rounds was performed, up to a maximum number defined by the user. This method allowed BEAP to stop the re-iterative BLAST process if no new sequences were retrieved, reducing the amount of time needed to complete a BEAP assembly. A progress summary was kept in the log file throughout the process to keep track of sequences retrieved and corresponding statistics such as sequence ID, database or origin, number of bases, E-value, etc
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