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© Oxford University Press

A tool for aligning very similar DNA sequences

Kun-Mao Chao , Jinghui Zhang 1, James Ostell 1 and Webb Miller 2,3

Department of Computer Science and Information Management, Providence University Shalu, Taichung, Taiwan 43309
1National Center for Biotechnology Information, National Library of Medicine NIH, Bethesda, MD 20894
2Department of Computer Science and Engineering, The Pennsylvania State University, University Park PA 16802, USA

3To whom correspondence should be addressed

Results: We have produced a computer program, named sim3, that solves the following computational problem. Two DNA sequences are given, where the shorter sequence is very similar to some contiguous region of the longer sequence. Sim3 determines such a similar region of the longer sequence, and then computes an optimal set of single-nucleotide changes (i.e. insertions, deletions or substitutions) that will convert the shorter sequence to that region. Thus, the alignment scoring scheme is designed to model sequencing errors, rather than evolutionary processes. The program can align a 100 kb sequence to a 1 megabase sequence in a few seconds on a workstation, provided that there are very few differences between the shorter sequence and some region in the longer sequence. The program has been used to assemble sequence data for the Genomes Division at the National Center for Biotechnology Information.

Availability: A version of sim3 for UNIX machines can be obtained by anonymous ftp from ncbi. nlm. nih. gov, in the pub/sim3 directory.

Contact: For portable versions for Macs and PCs, contact zjing@sunset. nlm. nih. gov.

Received on August 14, 1996; accepted on October 8, 1996

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