loading
Documents

Research.Publish.Connect.

Paper

Paper Unlock

Authors: Anna Gambin 1 ; Sławomir Lasota 2 ; Michał Startek 2 ; Maciej Sykulski 2 ; Laurent Noé 3 and Gregory Kucherov 3

Affiliations: 1 University of Warsaw and Mossakowski Medical Research Centre Polish Academy of Sciences, Poland ; 2 University of Warsaw, Poland ; 3 LIFL/CNRS/INRIA, France

ISBN: 978-989-8425-36-2

Keyword(s): Sequence alignment, Protein BLAST, Subset seed, DFA, Genetic algorithm.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Sequence Analysis

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/s blast. Supplementary material and user manual are also provided. (More)

PDF ImageFull Text

Download
Sign In Guest: Register as new SciTePress user now for free.

Sign In SciTePress user: please login.

PDF ImageMy Papers

You are not signed in, therefore limits apply to your IP address 54.161.49.216

In the current month:
Recent papers: 100 available of 100 total
2+ years older papers: 200 available of 200 total

Paper citation in several formats:
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

@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},
}

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

Login or register to post comments.

Comments on this Paper: Be the first to review this paper.