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Authors: André Atanasio M. Almeida and Zanoni Dias

Affiliation: University of Campinas, Brazil

Keyword(s): Multiple sequence alignment, K-mer count method, Compressed alphabet.

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

Abstract: Sequence alignment is the most common task in the bioinformatics field. It is a required method for the execution of a wide range of procedures such as the search for homologue sequences in a database or protein structure prediction. The main goal of the experiments in this work was to improve on the accuracy of the multiple sequence alignments. Our experiments concentrated on the MUMMALS multiple aligner, experimenting with three distinct modifications to the algorithm. Our first experiment was to modify the substring length of the k-mer count method. The second experiment we attempted was to substitute the commonly used Dayhoff(6) with alternative compressed alphabets. The third experiment was to modify the distance matrix computation and the guide tree construction. Each of the experiments showed a gain in result accuracy.

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Paper citation in several formats:
Atanasio M. Almeida, A. and Dias, Z. (2012). IMPROVEMENTS TO A MULTIPLE PROTEIN SEQUENCE ALIGNMENT TOOL. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2012) - BIOINFORMATICS; ISBN 978-989-8425-90-4; ISSN 2184-4305, SciTePress, pages 226-233. DOI: 10.5220/0003789202260233

@conference{bioinformatics12,
author={André {Atanasio M. Almeida}. and Zanoni Dias.},
title={IMPROVEMENTS TO A MULTIPLE PROTEIN SEQUENCE ALIGNMENT TOOL},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2012) - BIOINFORMATICS},
year={2012},
pages={226-233},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003789202260233},
isbn={978-989-8425-90-4},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2012) - BIOINFORMATICS
TI - IMPROVEMENTS TO A MULTIPLE PROTEIN SEQUENCE ALIGNMENT TOOL
SN - 978-989-8425-90-4
IS - 2184-4305
AU - Atanasio M. Almeida, A.
AU - Dias, Z.
PY - 2012
SP - 226
EP - 233
DO - 10.5220/0003789202260233
PB - SciTePress

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