Skip Navigation

Nucleic Acids Research 2005 33(13):4335-4344; doi:10.1093/nar/gki739
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (143K) Freely available
Right arrow Screen PDF (145K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (2)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Kim, Y. J.
Right arrow Articles by Patel, J. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Kim, Y. J.
Right arrow Articles by Patel, J. M.
Related Collections
Right arrow Computational methods
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 1 August 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST

You Jung Kim, Andrew Boyd1, Brian D. Athey1 and Jignesh M. Patel*

Department of Electrical Engineering and Computer Science, University of Michigan Ann Arbor, MI 48109, USA 1Michigan Center for Biological Information, University of Michigan 3600 Green Court, Ann Arbor, MI 48109, USA

*To whom correspondence should be addressed. Tel: +1 734 647 1806; Fax: +1 734 763 8094; Email: jignesh{at}eecs.umich.edu

Received March 18, 2005. Revised May 26, 2005. Accepted July 11, 2005.

A common task in many modern bioinformatics applications is to match a set of nucleotide query sequences against a large sequence dataset. Exis-ting tools, such as BLAST, are designed to evaluate a single query at a time and can be unacceptably slow when the number of sequences in the query set is large. In this paper, we present a new algorithm, called miBLAST, that evaluates such batch workloads efficiently. At the core, miBLAST employs a q-gram filtering and an index join for efficiently detecting similarity between the query sequences and database sequences. This set-oriented technique, which indexes both the query and the database sets, results in substantial performance improvements over existing methods. Our results show that miBLAST is significantly faster than BLAST in many cases. For example, miBLAST aligned 247 965 oligonucleotide sequences in the Affymetrix probe set against the Human UniGene in 1.26 days, compared with 27.27 days with BLAST (an improvement by a factor of 22). The relative performance of miBLAST increases for larger word sizes; however, it decreases for longer queries. miBLAST employs the familiar BLAST statistical model and output format, guaranteeing the same accuracy as BLAST and facilitating a seamless transition for existing BLAST users.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
W. Qu, Z. Shen, D. Zhao, Y. Yang, and C. Zhang
MFEprimer: multiple factor evaluation of the specificity of PCR primers
Bioinformatics, January 15, 2009; 25(2): 276 - 278.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. G. Tarcea, T. Weymouth, A. Ade, A. Bookvich, J. Gao, V. Mahavisno, Z. Wright, A. Chapman, M. Jayapandian, A. Ozgur, et al.
Michigan molecular interactions r2: from interacting proteins to pathways
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D642 - D646.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. Morgulis, G. Coulouris, Y. Raytselis, T. L. Madden, R. Agarwala, and A. A. Schaffer
Database indexing for production MegaBLAST searches
Bioinformatics, August 15, 2008; 24(16): 1757 - 1764.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Jayapandian, A. Chapman, V. G. Tarcea, C. Yu, A. Elkiss, A. Ianni, B. Liu, A. Nandi, C. Santos, P. Andrews, et al.
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D566 - D571.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.