Title: A direct method for computing extreme value (Gumbel) parameters for gapped biological sequence alignments

Authors: Terrance Quinn; Zachariah Sinkala

Addresses: Department of Mathematical Sciences, Middle Tennessee State University, 1301 E. Main Street, Murfreesboro, TN 37132, USA ' Department of Mathematical Sciences, Middle Tennessee State University, 1301 E. Main Street, Murfreesboro, TN 37132, USA

Abstract: We develop a general method for computing extreme value distribution (Gumbel, 1958) parameters for gapped alignments. Our approach uses mixture distribution theory to obtain associated BLOSUM matrices for gapped alignments, which in turn are used for determining significance of gapped alignment scores for pairs of biological sequences. We compare our results with parameters already obtained in the literature.

Keywords: bioinformatics; biological sequences; sequence alignment; BLOSUM matrix; direct method; extreme value distribution; gapped alignment; mixture method; Gumbel distribution.

DOI: 10.1504/IJBRA.2014.059517

International Journal of Bioinformatics Research and Applications, 2014 Vol.10 No.2, pp.177 - 189

Received: 07 Feb 2011
Accepted: 15 Feb 2012
Published online: 24 Oct 2014 *

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