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2005
IEEE

Suboptimal Alignments Improve the Detection of Weak Homologs in Sequence Database Searches

9 years 7 months ago
Suboptimal Alignments Improve the Detection of Weak Homologs in Sequence Database Searches
PSI-BLAST remains one of the popular tools for searching remote homologs in sequence databases. We recently demonstrated that hybrid alignment can function as the alignment core for PSI-BLAST without loss of sensitivity. Here, we start to exploit the benefits of hybrid alignment. We show that incorporating information about the suboptimal alignments, otherwise ignored in PSI-BLAST, already improves the sensitivity of our enhanced version of PSIBLAST. More interestingly, we find a set of sequences on which our tool disagrees with the classification given by SCOP. Careful examination points to a possible misclassification in SCOP. Cross-referencing with two other methods of protein structure classification, CATH and DALI, supports this view, indicating that the enriched information from suboptimal alignments is valuable for detecting more weakly homologous sequences. KEYWORD: sequence alignment, hybrid algorithm, PSI-BLAST, suboptimal alignment, forward-backward algorithm
Yuheng Li, Mario Lauria, Ralf Bundschuh
Added 24 Jun 2010
Updated 24 Jun 2010
Type Conference
Year 2005
Where BIBE
Authors Yuheng Li, Mario Lauria, Ralf Bundschuh
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