Exploring science is typically characterized by a lot of puzzles, frustrations or even failures. This weblog is mainly intended to record my working, thinking and knowledge acquisitions. I expect that some reflection would refresh my mind from time to time, and motivate me to move further, and hopefully give me a better view about even changing the landscape of bioinformatics.
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Tuesday, December 28, 2010
A performance enhanced PSI-BLAST based on hybrid alignment
Motivation: 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.