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Authors: Kalle Karhu 1 ; Juho Mäkinen 1 ; Jussi Rautio 1 ; Jorma Tarhio 1 and Hugh Salamon 2

Affiliations: 1 Aalto University, Finland ; 2 AbaSci and LLC, United States

Keyword(s): Sequence alignment, Text algorithms, Indexing.

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

Abstract: Alignment to a genomic sequence is a common task in modern bioinformatics. By improving the methods used, significant amount of time and resources can be saved. We have developed a new genomic alignment search tool, called GAST, for sequences of at least 160 nt. GAST is many times faster than commonly used alignment tools BLAT and Mega BLAST. As the sizes of query sequences and the database increase, the advantage grows. This paper describes the principles of GAST and reports a comparison of GAST with BLAT and Mega BLAST. The effects the query sequence length and the number of queries have on run times were studied using the full human genome and the chromosome 1 of human genome separately. Additionally, the error tolerance and behaviour of GAST when handling sequences with lower similarity to a database was studied. Lastly, we compared the quality of exon mappings produced by the three tools and the genomic mapping tool GMAP.

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Paper citation in several formats:
Karhu, K.; Mäkinen, J.; Rautio, J.; Tarhio, J. and Salamon, H. (2011). GAST, A GENOMIC ALIGNMENT SEARCH TOOL. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2011) - BIOINFORMATICS; ISBN 978-989-8425-36-2; ISSN 2184-4305, SciTePress, pages 82-90. DOI: 10.5220/0003181400820090

@conference{bioinformatics11,
author={Kalle Karhu. and Juho Mäkinen. and Jussi Rautio. and Jorma Tarhio. and Hugh Salamon.},
title={GAST, A GENOMIC ALIGNMENT SEARCH TOOL},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2011) - BIOINFORMATICS},
year={2011},
pages={82-90},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003181400820090},
isbn={978-989-8425-36-2},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2011) - BIOINFORMATICS
TI - GAST, A GENOMIC ALIGNMENT SEARCH TOOL
SN - 978-989-8425-36-2
IS - 2184-4305
AU - Karhu, K.
AU - Mäkinen, J.
AU - Rautio, J.
AU - Tarhio, J.
AU - Salamon, H.
PY - 2011
SP - 82
EP - 90
DO - 10.5220/0003181400820090
PB - SciTePress

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