SUBSET SEED EXTENSION TO PROTEIN BLAST

Anna Gambin, Sławomir Lasota, Michał Startek, Maciej Sykulski, Laurent Noé, Gregory Kucherov

2011

Abstract

The seeding technique became central in the theory of sequence alignment and there are several efficient tools applying seeds to DNA homology search. Recently, a concept of subset seeds has been proposed for similarity search in protein sequences. We experimentally evaluate the applicability of subset seeds to protein homology search. We advocate the use of multiple subset seeds derived from a hierarchical tree of amino acid residues. Our method computes, by an evolutionary algorithm, seeds that are specifically designed for a given protein family. The representation of seeds by deterministic finite automata (DFAs) is developed and built into the NCBI-BLAST software. This extended tool, named SeedBLAST, is compared to the original NCBI-BLAST on the GPCR protein family. Our results demonstrate a clear superiority of SeedBLAST in terms of efficiency, especially in the case of twilight zone hits. SeedBLAST is an open source software freely available http://bioputer.mimuw.edu.pl/papers/sblast. Supplementary material and user manual are also provided.

Paper Citation

in Harvard Style

Gambin A., Lasota S., Startek M., Sykulski M., Noé L. and Kucherov G. (2011). SUBSET SEED EXTENSION TO PROTEIN BLAST . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011) ISBN 978-989-8425-36-2, pages 149-158. DOI: 10.5220/0003147601490158

in Bibtex Style

@conference{bioinformatics11,
author={Anna Gambin and Sławomir Lasota and Michał Startek and Maciej Sykulski and Laurent Noé and Gregory Kucherov},
title={SUBSET SEED EXTENSION TO PROTEIN BLAST},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)},
year={2011},
pages={149-158},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003147601490158},
isbn={978-989-8425-36-2},
}

in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)
TI - SUBSET SEED EXTENSION TO PROTEIN BLAST
SN - 978-989-8425-36-2
AU - Gambin A.
AU - Lasota S.
AU - Startek M.
AU - Sykulski M.
AU - Noé L.
AU - Kucherov G.
PY - 2011
SP - 149
EP - 158
DO - 10.5220/0003147601490158