Paper Info
Title
Using Hybrid Alignment for Iterative Sequence Database Searches
Abstract
Progressive sequence model refinement by means of iterative searches is an effective technique for high sensitivity database searches and is currently employed in popular tools such as PSI-BLAST and SAM. Recently, a novel alignment algorithm has been proposed that offers features expected to improve the sensitivity of such iterative approaches, specifically a well-characterized theory of its statistics even in the presence of position-specific gap costs. Here, we demonstrate that the new hybrid alignment algorithm is ready to be used as the alignment core of PSI-BLAST. In addition, we evaluate the accuracy of two proposed approaches to edge effect correction in short sequence alignment statistics that turns out to be one of the crucial issues in developing a hybrid-alignment based version of PSI-BLAST.
Year
DOI
Venue
2004
10.1002/cpe.809
Concurrency and Computation: Practice and Experience
Keywords
DocType
Volume
hybrid alignment,crucial issue,high sensitivity database search,short sequence alignment statistic,iterative approach,new hybrid alignment algorithm,alignment core,progressive sequence model refinement,iterative sequence database searches,iterative search,novel alignment algorithm,genomics,iterative methods,parallel algorithms,database search,bioinformatics,proteomics,information science,edge effect,statistics,sequences,genomes
Journal
16
Issue
ISSN
ISBN
9
1532-0626
0-7695-1926-1
Citations 
PageRank 
References 
2
0.39
12
Authors
3
Name
Order
Citations
PageRank
Yuheng Li1584.84
Mario Lauria262895.12
Ralf Bundschuh37713.85