Multiple Sequence Alignment System for Pyrosequencing Reads

  • Fahad Saeed
  • Ashfaq Khokhar
  • Osvaldo Zagordi
  • Niko Beerenwinkel
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5462)


Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as Sanger. However, the reads generated by pyrosequencing are short in size and contain numerous errors. In order to use these reads for any subsequent analysis, the reads must be aligned . Existing multiple sequence alignment methods cannot be used as they do not take into account the specific positions of the sequences with respect to the genome, and are highly inefficient for large number of sequences. Therefore, the common practice has been to use either simple pairwise alignment despite its poor accuracy for error prone pyroreads, or use computationally expensive techniques based on sequential gap propagation. In this paper, we develop a computationally efficient method based on domain decomposition, referred to as pyro-align, to align such large number of reads. The proposed alignment algorithm accurately aligns the erroneous reads in a short period of time, which is orders of magnitude faster than any existing method. The accuracy of the alignment is confirmed from the consensus obtained from the multiple alignments.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Fahad Saeed
    • 1
  • Ashfaq Khokhar
    • 1
  • Osvaldo Zagordi
    • 2
  • Niko Beerenwinkel
    • 2
  1. 1.Department of Electrical and Computer EngineeringUniversity of Illinois at ChicagoUSA
  2. 2.Department of Biosystems Science and EngineeringETH ZurichBaselSwitzerland

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