Please use this identifier to cite or link to this item: http://scholarbank.nus.edu.sg/handle/10635/104612
Title: Procrastination leads to efficient filtration for local multiple alignment
Authors: Darling, A.E.
Treangen, T.J.
Zhang, L. 
Kuiken, C.
Messeguer, X.
Perna, N.T.
Issue Date: 2006
Citation: Darling, A.E.,Treangen, T.J.,Zhang, L.,Kuiken, C.,Messeguer, X.,Perna, N.T. (2006). Procrastination leads to efficient filtration for local multiple alignment. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 4175 LNBI : 126-137. ScholarBank@NUS Repository.
Abstract: We describe an efficient local multiple alignment filtration heuristic for identification of conserved regions in one or more DNA sequences. 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 resulting local multiple alignments may have nucleotide substitutions and internal gaps as large as w characters in any occurrence of the motif. The algorithm consumes script O sign(wN] memory and script O sign(wN\ogwN) time where N is the sequence length. We score the significance of multiple alignments using entropy-based motif scoring methods. We demonstrate the performance 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 © Springer-Verlag Berlin Heidelberg 2006.
Source Title: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
URI: http://scholarbank.nus.edu.sg/handle/10635/104612
ISBN: 3540395830
ISSN: 03029743
Appears in Collections:Staff Publications

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