New Zealand Journal of Botany abstracts

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The expected number of matches in optimal global sequence alignments

INGRID RINSMA-MELCHERT

Department of Mathematics and Statistics
University of Waikato
Private Bag 3105
Hamilton, New Zealand

Abstract Sequence comparison is used in molecular biology to detect and characterise the homology between two or more sequences. Many optimal alignment algorithms have been developed to produce the alignment with least overall cost. However, each of these methods depend upon the relative cost of a null being given a priori. This cost has usually been determined by simulation or Monte Carlo methods or chosen to give "biologically interesting" results. This paper outlines how lattice walks and generating functions could be used to find the expected number of matches in the optimal alignment of two sequences, in several special cases. Solving the resulting equations proves difficult.

Keywords optimal alignment; sequence alignment; DNA sequence alignment; generating functions; lattice walks

B93014 ; Received 2 February 1993; accepted 5 July 1993
New Zealand Journal of Botany, 1993, Vol. 31: 219-230 219
0028-825X/93/3103-0219 $2.50/0 © The Royal Society of New Zealand 1993

PDF file of entire paper: medium quality (635K); (scanned from paper original: notes about this process)

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