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Bioinformatics Vol. 18 no. 6 2002
Pages 886-887
© 2002 Oxford University Press

Applications Note

Synonymous–non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN)

Matthew J. Gonzales 1, Jonathan M. Dugan 2 and Robert W. Shafer 1,*

1 Division of Infectious Diseases
2 Stanford Medical Informatics, Stanford University Medical Center, 300 Pasteur Drive, Room S-156, Stanford, CA 94305, USA

Received on August 23, 2001 ; revised on November 22, 2001 and January 7, 2002 ; accepted on January 9, 2002

Summary: Direct PCR sequencing on genetic material containing allelic mixtures results in sequences containing ambiguous nucleotides. Because codons exhibiting allelic mixtures present evidence of evolutionary pressure, it is important to include this information in the assessment of codon synonymy. We developed a program, ‘Synonymous–Nonsynonymous Mutation Rates between Sequences Containing Ambiguous Nucleotides’ (Syn-SCAN), that calculates synonymous and non-synonymous substitution rates using a model that includes allelic mixtures.

Availability: Syn-SCAN is implemented on the web and can be downloaded from http://hivdb.stanford.edu

Contact: rshafer{at}cmgm.stanford.edu

* To whom correspondence should be addressed.


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