Database indexing for production MegaBLAST searches.

ABSTRACT:

Motivation

The BLAST software package for sequence comparison speeds up homology search by preprocessing a query sequence into a lookup table. Numerous research studies have suggested that preprocessing the database instead would give better performance. However, production usage of sequence comparison methods that preprocess the database has been limited to programs such as BLAT and SSAHA that are designed to find matches when query and database subsequences are highly similar.

Results

We developed a new version of the MegaBLAST module of BLAST that does the initial phase of finding short seeds for matches by searching a database index. We also developed a program makembindex that preprocesses the database into a data structure for rapid seed searching. We show that the new

SUBMITTER: Morgulis A 

PROVIDER: S-EPMC2696921 | biostudies-literature | 2008 Aug

REPOSITORIES: biostudies-literature