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MBE Advance Access originally published online on May 30, 2003
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Mol. Biol. Evol. 20(8):1299-1309. 2003
DOI: 10.1093/molbev/msg139
© 2003 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

GS-Aligner: A Novel Tool for Aligning Genomic Sequences Using Bit-Level Operations

Arthur Chun-Chieh Shih*,{dagger} and Wen-Hsiung Li{dagger},{ddagger},

* Institute of Information Science, Academia Sinica, Taipei, Taiwan
{dagger} Department of Ecology and Evolution, University of Chicago
{ddagger} Genomics Research Center, Academia Sinica, Taipei, Taiwan

E-mail: whli{at}uchicago.edu.

A novel algorithm, GS-Aligner, that uses bit-level operations was developed for aligning genomic sequences. GS-Aligner is efficient in terms of both time and space for aligning two very long genomic sequences and for identifying genomic rearrangements such as translocations and inversions. It is suitable for aligning fairly divergent sequences such as human and mouse genomic sequences. It consists of several efficient components: bit-level coding, search for matching segments between the two sequences as alignment anchors, longest increasing subsequence (LIS), and optimal local alignment. Efforts have been made to reduce the execution time of the program to make it truly practical for aligning very long sequences. Empirical tests suggest that for relatively divergent sequences such as sequences from different mammalian orders or from a mammal and a nonmammalian vertebrate GS-Aligner performs better than existing methods. The program and data can be downloaded from http://pondside.uchicago.edu/~lilab/ and http://webcollab.iis.sinica.edu.tw/~biocom.

Key Words: genomic sequences • sequence alignment • conserved regions • translocations • inversions


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