GenBlastA: enabling BLAST to identify homologous gene sequences.
BLAST is an extensively used local similarity search tool for identifying homologous sequences. When a gene sequence (either protein sequence or nucleotide sequence) is used as a query to search for homologous sequences in a genome, the search results, represented as a list of high-scoring pairs (HSPs), are fragments of candidate genes rather than full-length candidate genes. Relevant HSPs ("signals"), which represent candidate genes in the target genome sequences, are buried within a report that contains also hundreds to thousands of random HSPs ("noises"). Consequently, BLAST results are often overwhelming and confusing even to experienced users. For effective use of BLAST, a program is needed for extracting relevant HSPs that represent candidate homologous genes from the entire HSP report. To achieve this goal, we have designed a graph-based algorithm, genBlastA, which automatically filters HSPs into well-defined groups, each representing a candidate gene in the target genome. The novelty of genBlastA is an edge length metric that reflects a set of biologically motivated requirements so that each shortest path corresponds to an HSP group representing a homologous gene. We have demonstrated that this novel algorithm is both efficient and accurate for identifying homologous sequences, and that it outperforms existing approaches with similar functionalities.
School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada.
Rong
R
She
Jeffrey S-C
JS
Chu
Ke
K
Wang
Jian
J
Pei
Nansheng
N
Chen
D000465:Algorithms; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D030541:Databases, Genetic; D049751:Genome, Helminth; D023281:Genomics / Q000706:statistics & numerical data; D006801:Humans; D016415:Sequence Alignment / Q000706:statistics & numerical data*; D012689:Sequence Homology, Nucleic Acid; D012984:Software