Int. J. of Bioinformatics Research and Applications   »   2014 Vol.10, No.2

 

 

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

 

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

 

Available online: 25 Feb 2014

 

 

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