A performance enhanced PSI-BLAST based on hybrid alignment.
BACKGROUND
Sequence alignment is one of the most popular tools of modern biology. NCBI's PSI-BLAST utilizes iterative model building in order to better detect distant homologs with greater sensitivity than non-iterative BLAST. However, PSI-BLAST's performance is limited by the fact that it relies on deterministic alignments. Using a semi-probabilistic alignment scheme such as Hybrid alignment should allow for better informed model building and improved identification of homologous sequences, particularly remote homologs.


RESULTS
We have built a new version of the tool in which the Smith-Waterman alignment algorithm core is replaced by the hybrid alignment algorithm. The favorable statistical properties of the hybrid algorithm allow the introduction of position-specific gap penalties in Hybrid PSI-BLAST. This improves the position-specific modeling of protein families and results in an overall improvement of performance.


BACKGROUND
Source code is freely available for download at http://bioserv.mps.ohio-state.edu/HybridPSI, implemented in C and supported on linux.
Covidien, 60 Middletown Avenue, North Haven, CT 06473, USA.
Yuheng
Y
Li
Nicholas
N
Chia
Mario
M
Lauria
Ralf
R
Bundschuh
D000465:Algorithms; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D017385:Sequence Homology; D012984:Software