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Parallel Syntenic Alignments

  • Natsuhiko Futamura
  • Srinivas Aluru
  • Xiaoqiu Huang
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2552)

Abstract

Given two genomic DNA sequences, the syntenic alignment problem is to compute an ordered list of subsequences for each sequence such that the corresponding subsequence pairs exhibit a high degree of similarity. Syntenic alignments are useful in comparing genomic DNA from related species andin identifying conservedgen es. In this paper, we present a parallel algorithm for computing syntenic alignments that runs in O(mn/p) time and O(m + n/p) memory per processor, where m and n are the respective lengths of the two genomic sequences. Our algorithm is time optimal with respect to the corresponding sequential algorithm and can use O(n/log n) processors, where n is the length of the larger sequence. Using an implementation of this parallel algorithm, we report the alignment of human chromosome 12p13 andit s syntenic region in mouse chromosome 6 (both over 220, 000 base pairs in length) in under 24 minutes on a 64-processor IBM xSeries cluster.

Keywords

Parallel Algorithm Optimal Alignment Syntenic Region Human Chromosome 12p13 Special Column 
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 2002

Authors and Affiliations

  • Natsuhiko Futamura
    • 1
  • Srinivas Aluru
    • 1
  • Xiaoqiu Huang
    • 1
  1. 1.Iowa State UniversityAmesUSA

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