Procrastination leads to efficient filtration for local multiple alignment

Procrastination leads to efficient filtration for local multiple alignment (2006)

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by Aaron E. Darling , Todd J. Treangen , Louxin Zhang , Carla Kuiken , Xavier Messeguer , Nicole T. Perna

Venue:	PROCEEDINGS OF THE 6TH INTERNATIONAL WORKSHOP ON ALGORITHMS IN BIOINFORMATICS (WABI)
Citations:	3 - 3 self

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Datum	Value	Source
TITLE	Procrastination leads to efficient filtration for local multiple alignment	user correction
AUTHOR NAME	Aaron E. Darling	user correction
AUTHOR AFFIL	1 Dept. of Computer Science, Univ. of Wisconsin-Madison, USA	user correction
AUTHOR NAME	Todd J. Treangen	user correction
AUTHOR AFFIL	2 Dept. of Computer Science, Technical Univ. of Catalonia, Barcelona	user correction
AUTHOR ADDR	Spain	user correction
AUTHOR NAME	Louxin Zhang	user correction
AUTHOR NAME	Carla Kuiken	user correction
AUTHOR NAME	Xavier Messeguer	user correction
AUTHOR NAME	Nicole T. Perna	user correction
AUTHOR AFFIL	5 T-10 Theoretical Biology Division, Los Alamos National Laboratory, USA	user correction
ABSTRACT	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	user correction
YEAR	2006	user correction
VENUE	PROCEEDINGS OF THE 6TH INTERNATIONAL WORKSHOP ON ALGORITHMS IN BIOINFORMATICS (WABI)	user correction
VENUE TYPE	CONFERENCE	user correction
PAGES	126--137	user correction
VOLUME	4175	user correction
CITATIONS	28 found	ParsCit 1.0