Chaining Algorithms for Alignment of Draft Sequence

  • Mukund Sundararajan
  • Michael Brudno
  • Kerrin Small
  • Arend Sidow
  • Serafim Batzoglou
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3240)


In this paper we propose a chaining method that can align a draft genomic sequence against a finished genome. We introduce the use of an overlap tree to enhance the state information available to the chaining procedure in the context of sparse dynamic programming, and demonstrate that the resulting procedure more accurately penalizes the various biological rearrangements. The algorithm is tested on a whole genome alignment of seven yeast species. We also demonstrate a variation on the algorithm that can be used for co-assembly of two genomes and show how it can improve the current assembly of the Ciona savignyi (sea squirt) genome.


Local Alignment Global Alignment Genome Alignment Draft Sequence Binary Search Tree 
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

  • Mukund Sundararajan
    • 1
  • Michael Brudno
    • 1
  • Kerrin Small
    • 2
  • Arend Sidow
    • 2
    • 3
  • Serafim Batzoglou
    • 1
  1. 1.Department of Computer ScienceStanford UniversityStanfordUSA
  2. 2.Department of GeneticsStanford UniversityStanfordUSA
  3. 3.Department of PathologyStanford UniversityStanfordUSA

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