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Bioinformatics Vol. 19 no. 2 2003
Pages 228-233
© 2003 Oxford University Press

A generalized global alignment algorithm

Xiaoqiu Huang 1,* and Kun-Mao Chao 2

1 Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA 50011-1040, USA
2 Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan

Received on May 27, 2002 ; revised on August 28, 2002 ; accepted on September 2, 2002

Motivation: Homologous sequences are sometimes similar over some regions but different over other regions. Homologous sequences have a much lower global similarity if the different regions are much longer than the similar regions.

Results: We present a generalized global alignment algorithm for comparing sequences with intermittent similarities, an ordered list of similar regions separated by different regions. A generalized global alignment model is defined to handle sequences with intermittent similarities. A dynamic programming algorithm is designed to compute an optimal general alignment in time proportional to the product of sequence lengths and in space proportional to the sum of sequence lengths. The algorithm is implemented as a computer program named GAP3 (Global Alignment Program Version 3). The generalized global alignment model is validated by experimental results produced with GAP3 on both DNA and protein sequences. The GAP3 program extends the ability of standard global alignment programs to recognize homologous sequences of lower similarity.

Availability: The GAP3 program is freely available for academic use at http://bioinformatics.iastate.edu/aat/align/align.html.

Contact: xqhuang{at}cs.iastate.edu; kmchao{at}csie.ntu.edu.tw

* To whom correspondence should be addressed.


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