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Improved Alignment of Protein Sequences Based on Common Parts

  • David Hoksza
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4983)

Abstract

In the last twenty years, protein databases have been growing exponentially. To speed up the search, heuristic approaches have been proposed and their accuracy has been steadily growing, but exact search is still needed in some cases. The only exact search algorithm remains SSEARCH (or it’s clones) which sequentially scans database of protein sequences, and performs full alignment against each of the sequences.

Due to the need of the exact search, we focus on improving the sequential search algorithm. We decrease the costs needed to compute the alignment of pair of protein sequences when used with large databases. This is achieved by reusing alignment calculations of common parts of the sequences without loss of accuracy.

With this method, we reduced the computational costs by up to 20 % depending on the database size and subset used. We also implemented approximate search which further reduced computational costs for the the sake of some accuracy loss.

Keywords

protein databases Smith-Waterman algorithm 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • David Hoksza
    • 1
  1. 1.Department of software engineering, Faculty of Mathematics and PhysicsCharles University in PraguePrague 1Czech Republic

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