Conference Paper

Procrastination Leads to Efficient Filtration for Local Multiple Alignment.

DOI: 10.1007/11851561_12 Conference: Algorithms in Bioinformatics, 6th International Workshop, WABI 2006, Zurich, Switzerland, September 11-13, 2006, Proceedings
Source: DBLP

ABSTRACT We describe an efficient local multiple alignment filtration heuristic for identification of conserved regions in one or more DNA se- quences. The method incorporates several novel ideas: (1) palindromic spaced seed patterns to match both DNA strands simultaneously, (2) seed extension (chaining) in order of decreasing multiplicity, and (3) procrastination when low multiplicity matches are encountered. The re- sulting local multiple alignments may have nucleotide substitutions and internal gaps as large as w characters in any occurrence of the motif. The algorithm consumes O(wN) memory and O(wN log wN) time where N is the sequence length. We score the significance of multiple alignments using entropy-based motif scoring methods. We demonstrate the per- formance of our filtration method on Alu-repeat rich segments of the human genome and a large set of Hepatitis C virus genomes. The GPL implementation of our algorithm in C++ is called procrastAligner and is freely available from http://gel.ahabs.wisc.edu/procrastination

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