Database indexing for production MegaBLAST searches
National Institutes of Health · National Center for Biotechnology Information
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…
Citation impact
- FWCI
- 4.63
- Percentile
- 100%
- References
- 19
Authors
6- AMAleksandr MorgulisCorresponding
National Institutes of Health, National Center for Biotechnology Information
- GCGeorge Coulouris
National Institutes of Health, National Center for Biotechnology Information
- YRYan Raytselis
National Institutes of Health, National Center for Biotechnology Information
- TMThomas Madden
National Institutes of Health, National Center for Biotechnology Information
- RARicha Agarwala
National Institutes of Health, National Center for Biotechnology Information
Topics & keywords
- Computer science
- Database
- Search engine indexing
- Preprocessor
- Sequence database
- Information retrieval
- Database index
- Data mining