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Multiple Vector Seeds for Protein Alignment

  • Daniel G. Brown
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3240)

Abstract

We present a framework for improving local protein alignment algorithms. Specifically, we discuss how to extend local protein aligners to use a collection of vector seeds [3] to reduce noise hits. We model picking a set of vector seeds as an integer programming problem, and give algorithms to choose such a set of seeds. A good set of vector seeds we have chosen allows four times fewer false positive hits, while preserving essentially identical sensitivity as BLASTP.

Keywords

False Positive Rate Protein Alignment True Alignment Nucleotide Alignment Unrelated Sequence 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Daniel G. Brown
    • 1
  1. 1.School of Computer ScienceUniversity of WaterlooWaterlooCanada

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