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Blast++: A Tool for Blasting Queries in Batches

Source: OAI

ABSTRACT BLAST is the standard tool to search for sequence similarity in genomic (and protein) databases. It employs a brute force approach of comparing a query sequence against every database sequence - for each pair of the sequences to be matched, BLAST searches for short fixed-length word pairs (seeds) in the sequences and then extends them to higher-scoring regions. To search multiple queries, the basic approach is to run BLAST on each of the queries one at a time. This project presents a new sequence search tool BLAST++, which is implemented as an extension of the NCBI BLAST. BLAST++ essentially treats a collection of queries as a single virtual query so that the seed matching and seed extension step need to be performed only once for a batch of input query sequences. The study shows that BLAST++ is able to produce the same set of answers as BLAST (given the same settings), and yet able to achieve significant savings in computation cost as compared to BLAST. BLAST++ is also proved to achieve better sensitivity than BLAST while keeping up the speed.

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    05/2004;