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Using Hybrid Alignment for Iterative Sequence Database Searches

9 years 7 months ago
Using Hybrid Alignment for Iterative Sequence Database Searches
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 PSIBLAST. 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.
Yuheng Li, Mario Lauria, Ralf Bundschuh
Added 04 Jul 2010
Updated 04 Jul 2010
Type Conference
Year 2003
Where IPPS
Authors Yuheng Li, Mario Lauria, Ralf Bundschuh
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