Probabilistic alignment detects remote homology in a pair of protein sequences without homologous sequence information
Ryotaro Koike
Global Scientific Information and Computing Center, Tokyo Institute of Technology, Ookayama, Tokyo 152-8550, Japan
Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Japan
Search for more papers by this authorKengo Kinoshita
Structure and Function of Biomolecules, SORST, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
Search for more papers by this authorCorresponding Author
Akinori Kidera
International Graduate School of Arts and Sciences, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
Institute of Molecular Science, Okazaki, 444-8585, Japan
International Graduate School of Arts and Sciences, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan===Search for more papers by this authorRyotaro Koike
Global Scientific Information and Computing Center, Tokyo Institute of Technology, Ookayama, Tokyo 152-8550, Japan
Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Japan
Search for more papers by this authorKengo Kinoshita
Structure and Function of Biomolecules, SORST, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
Search for more papers by this authorCorresponding Author
Akinori Kidera
International Graduate School of Arts and Sciences, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
Institute of Molecular Science, Okazaki, 444-8585, Japan
International Graduate School of Arts and Sciences, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan===Search for more papers by this authorAbstract
Dynamic programming (DP) and its heuristic algorithms are the most fundamental methods for similarity searches of amino acid sequences. Their detection power has been improved by including supplemental information, such as homologous sequences in the profile method. Here, we describe a method, probabilistic alignment (PA), that gives improved detection power, but similarly to the original DP, uses only a pair of amino acid sequences. Receiver operating characteristic (ROC) analysis demonstrated that the PA method is far superior to BLAST, and that its sensitivity and selectivity approach to those of PSI-BLAST. Particularly for orphan proteins having few homologues in the database, PA exhibits much better performance than PSI-BLAST. On the basis of this observation, we applied the PA method to a homology search of two orphan proteins, Latexin and Resuscitation-promoting factor domain. Their molecular functions have been described based on structural similarities, but sequence homologues have not been identified by PSI-BLAST. PA successfully detected sequence homologues for the two proteins and confirmed that the observed structural similarities are the result of an evolutional relationship. Proteins 2007. © 2006 Wiley-Liss, Inc.
Supporting Information
The Supplementary Material referred to in this article can be found at http://www.interscience.wiley.com/jpages/0887-3585/suppmat/
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