An Almost Quadratic Time Algorithm for Sparse Spliced Alignment

The sparse spliced alignment problem consists of finding a chain of zero or more exons from O ( n ) prescribed candidate exons of a DNA sequence of length O ( n ) that is most similar to a known related gene sequence of length  n . This study improves the running time of the fastest known algorithm...

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Veröffentlicht in:Theory of computing systems Jg. 48; H. 1; S. 189 - 210
1. Verfasser: Sakai, Yoshifumi
Format: Journal Article
Sprache:Englisch
Veröffentlicht: New York Springer-Verlag 01.01.2011
Springer Nature B.V
Schlagworte:
Algorithms
Computer programming
Computer Science
Dynamic programming
Mathematical analysis
Studies
Theory of Computation
String algorithm
Common substring alignment
Semi-local string comparison
ISSN:1432-4350, 1433-0490
Online-Zugang:Volltext
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Zusammenfassung:The sparse spliced alignment problem consists of finding a chain of zero or more exons from O ( n ) prescribed candidate exons of a DNA sequence of length O ( n ) that is most similar to a known related gene sequence of length  n . This study improves the running time of the fastest known algorithm for this problem to date, which executes in O ( n 2.25 ) time, or very recently, in O ( n 2 log  2 n ) time, by proposing an O ( n 2 log  n )-time algorithm.
Bibliographie:SourceType-Scholarly Journals-1
ObjectType-Feature-1
content type line 14
ISSN:1432-4350
1433-0490
DOI:10.1007/s00224-009-9239-x