BLAST+: architecture and applications.

ABSTRACT:

Background

Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications.

Results

We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries agai

SUBMITTER: Camacho C 

PROVIDER: S-EPMC2803857 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature