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CHOP: visualization of 'wobbling' and isolation of highly conserved regions from aligned DNA sequences

Ohtsuka, M., Horiuchi, S., Kulski, J.K., Kimura, M. and Inoko, H. (2004) CHOP: visualization of 'wobbling' and isolation of highly conserved regions from aligned DNA sequences. Nucleic Acids Research, 32 (Web Server). W55-W58.

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Link to Open Access version: http://dx.doi.org/10.1093/nar/gkh448
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Abstract

The web software CHOP was developed to visualize the 'wobbling' in the third codon position of aligned DNA sequences. The simple features of this tool allow users to easily find regions suspected of containing coding sequences (CDSs). The program also allows visualization of the nucleotide diversity between two genomic or gene sequences by graphically plotting the percentage identity between the two sequences. CHOP can also isolate highly conserved regions within both CDSs and non-CDSs. Highly conserved regions within CDSs include the regions with lower rates of synonymous substitution in which nucleotide sequences are expected to be under strong selective pressure.

Publication Type: Journal Article
Murdoch Affiliation: School of Information Technology
Publisher: Oxford University Press
Copyright: © Oxford University Press 2004
URI: http://researchrepository.murdoch.edu.au/id/eprint/10124
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