Paper Info
Title
Suboptimal Alignments Improve the Detection of Weak Homologs in Sequence Database Searches
Abstract
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 PSI-BLAST. 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 misclassificationin 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.
Year
DOI
Venue
2005
10.1109/BIBE.2005.54
BIBE
Keywords
Field
DocType
sequence database searches,suboptimal alignment,popular tool,weak homologs,alignment core,careful examination point,protein structure classification,remote homologs,enriched information,possible misclassificationin,suboptimal alignments improve,enhanced version,hybrid alignment,forward backward algorithm,sequence alignment,molecular biophysics,proteins,hybrid algorithm,database search
Sequence alignment,Hybrid algorithm,Forward–backward algorithm,Sequence database,Alignment-free sequence analysis,Computer science,Bioinformatics,Multiple sequence alignment,Homologous Sequences
Conference
ISBN
Citations 
PageRank 
0-7695-2476-1
1
0.36
References 
Authors
11
3
Name
Order
Citations
PageRank
Yuheng Li1584.84
Mario Lauria262895.12
Ralf Bundschuh37713.85