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© Oxford University Press

SIMPLE34: an improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences

John M. Hancock and John S. Armstrong

Molecular Evolution and Systematics Group and Bioinformatics Facility, Research School of Biological Sciences, Australian National University Canberra, ACT 0200, Australia

SIMPLE34 is an improved and enhanced version of SIMPLE for Vax and SunOS systems. It now provides a length-independent measure of the overall level of tri- and tetra nucleotide motif clustering within nucleotide sequences and its significant deviation from random expectation. It now also provides information on tri- and tetranucleotide motifs showing higher levels of clustering than would be expected in random sequences. Sequence simplicity of test sequences can be judged with respect to random sequences generated on the basis of base composition, positional base composition or doublet frequency. These options can be used to investigate factors resulting in sequence simplicity.

Received on May 4, 1993; accepted on October 12, 1993

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