Research Article

Using hybrid alignment for iterative sequence database searches

  1. Yuheng Li1,
  2. Mario Lauria1,
  3. Ralf Bundschuh2,*

Article first published online: 6 JUL 2004

DOI: 10.1002/cpe.809

Issue

Concurrency and Computation: Practice and Experience

Concurrency and Computation: Practice and Experience

Special Issue: High Performance Computational Biology

Volume 16, Issue 9, pages 841–853, 10 August 2004

Additional Information

How to Cite

Li, Y., Lauria, M. and Bundschuh, R. (2004), Using hybrid alignment for iterative sequence database searches. Concurrency and Computation: Practice and Experience, 16: 841–853. doi: 10.1002/cpe.809

Author Information

  1. 1

    Department of Computer and Information Science, The Ohio State University, 2015 Neil Ave. #395, Columbus, OH 43210, U.S.A.

  2. 2

    Department of Physics, The Ohio State University, 174 West 18th Ave., Columbus, OH 43210, U.S.A.

*Department of Physics, The Ohio State University, 174 West 18th Ave., Columbus, OH 43210, U.S.A.

Publication History

  1. Issue published online: 6 JUL 2004
  2. Article first published online: 6 JUL 2004
  3. Manuscript Accepted: 8 SEP 2003
  4. Manuscript Received: 13 JUN 2003

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Keywords:

  • sequence alignment;
  • hybrid algorithm;
  • length correction;
  • PSI-BLAST;
  • MPI

Abstract

Progressive sequence model refinement by means of iterative searches is an effective technique for high sensitivity database searches and is currently employed in popular tools such as PSI-BLAST and SAM. Recently, a novel alignment algorithm has been proposed that offers features expected to improve the sensitivity of such iterative approaches, specifically a well-characterized theory of its statistics even in the presence of position-specific gap costs. Here, we demonstrate that the new hybrid alignment algorithm is ready to be used as the alignment core of PSI-BLAST. In addition, we evaluate the accuracy of two proposed approaches to edge effect correction in short sequence alignment statistics that turns out to be one of the crucial issues in developing a hybrid-alignment based version of PSI-BLAST. Copyright © 2004 John Wiley & Sons, Ltd.

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