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Bioinformatics Advance Access published online on June 19, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp372
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

GR-Aligner: an algorithm for aligning pairwise genomic sequences containing rearrangement events

Te-Chin Chu 1,2, Tsunglin Liu 3, D.T. Lee 1,4,5, Greg C. Lee 2 and Arthur Chun-Chieh Shih 1,4,*

1Institute of Information Science, 3Biodiversity Research Center and 4Research Center for Information Technology Innovation, Academia Sinica, Taipei, Taiwan
2Department of Computer Science and Information Engineering, National Taiwan Normal University, Taipei, Taiwan
5Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan

*To whom correspondence should be addressed. Dr. Arthur Shih, E-mail: arthur{at}iis.sinica.edu.tw


  Abstract

Motivation: Homologous genomic sequences between species usually contain different rearrangement events. Whether some specific patterns existed in the breakpoint regions that caused such events to occur is still unclear. To resolve this question, it is necessary to determine the location of breakpoints at the nucleotide level. The availability of sequences near breakpoints would further facilitate the related studies. We thus need a tool that can identify breakpoints and align the neighboring sequences. Although local alignment tools can detect rearrangement events, they only report a set of discontinuous alignments, where the detailed alignments in the breakpoint regions are usually missing. Global alignment tools are even less appropriate for these tasks since most of them are designed to align the conserved regions between sequences in a consistent order, i.e., they do not consider rearrangement events.

Results: We propose an effective and efficient pairwise sequence alignment algorithm, called GR-Aligner, which can find breakpoints of rearrangement events by integrating the forward and reverse alignments of the breakpoint regions flanked by homologously rearranged sequences. In addition, GR-Aligner also provides an option to view the alignments of sequences extended to the breakpoints. These outputs provide materials for studying possible evolutionary mechanisms and biological functionalities of the rearrangement.

Availability: http://biocomp.iis.sinica.edu.tw/new/GR_Aligner.htm

Contact: arthur{at}iis.sinica.edu.tw

Associate Editor: Prof. John Quackenbush

Received on January 12, 2009; revised on June 9, 2009; accepted on June 11, 2009

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