CHOP: visualization of ‘wobbling’ and isolation of highly conserved regions from aligned DNA sequences
Division of Basic Molecular Science and Molecular Medicine, School of Medicine, Tokai University, Bohseidai, Isehara, Kanagawa 259–1193, Japan and 1 Centre for Bioinformatics and Biological Computing, School of Information Technology, Murdoch University, Murdoch, 6150 Western Australia, Australia
* To whom correspondence should be addressed. Tel: +81 463 93 1121 (ext.) 2682; Fax: +81 463 96 2892; Email: masato{at}is.icc.u-tokai.ac.jp
Received February 11, 2004; Revised and Accepted April 20, 2004
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. CHOP is available at http://bunsei2.med.u-tokai.ac.jp:8080/~ohtsuka/cds_finding.html.
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