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A Heuristic Algorithm for Multiple Sequence Alignment Based on Blocks

Author

Listed:
  • Peng Zhao

    (IBM Toronto Lab)

  • Tao Jiang

    (University of California)

Abstract

Blocked multiple sequence alignment refers to the construction of multiple alignment by first aligning conserved regions into what we call “blocks” and then aligning the regions between successive blocks to form a final alignment. Instead of starting from low order pairwise alignments we propose a new way to form blocks by searching for closely related regions in all input sequences, allowing internal spaces in blocks as well as some degree of mismatch. We address the problem of semi-conserved patterns (patterns that do not appear in all input sequences) by introducing into the process two similarity thresholds that are adjusted dynamically according to the input. A method to control the number of blocks is also presented to deal with the situation when input sequences have so many similar regions that it becomes impractical to form blocks by trying every combination. BMA is an implementation of this approach, and our experimental results indicatethat this approach is efficient, particularly on large numbers of long sequences with well-conserved regions.

Suggested Citation

  • Peng Zhao & Tao Jiang, 2001. "A Heuristic Algorithm for Multiple Sequence Alignment Based on Blocks," Journal of Combinatorial Optimization, Springer, vol. 5(1), pages 95-115, March.
    • Handle: RePEc:spr:jcomop:v:5:y:2001:i:1:d:10.1023_a:1009841718561
    DOI: 10.1023/A:1009841718561
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    References listed on IDEAS

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    1. Laxmi Parida & Aris Floratos & Isidore Rigoutsos, 1999. "An Approximation Algorithm for Alignment of Multiple Sequences using Motif Discovery," Journal of Combinatorial Optimization, Springer, vol. 3(2), pages 247-275, July.
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