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Nucleic Acids Research, 2003, Vol. 31, No. 13 3682-3685
© 2003 Oxford University Press

TRACTS: a program to map oligopurine.oligopyrimidine and other binary DNA tracts

Moshe Gal, Tzvi Katz, Amir Ovadia and Gad Yagil*,1

BioMining Ltd, POB 2526, Kadima, Israel 1 Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel 76100

*To whom correspondence should be addressed. Tel: +972 89 460 918; Fax: +972 89 344 125; Email: gad.yagil{at}weizmann.ac.il

A program to map the locations and frequencies of DNA tracts composed of only two bases (‘Binary DNA’) is described. The program, TRACTS (URL http://bioportal.weizmann.ac.il/tracts/tracts.html and/or http://bip.weizmann.ac.il/miwbin/servers/tracts) is of interest because long tracts composed of only two bases are highly over-represented in most genomes. In eukaryotes, oligopurine.oligopyrimidine tracts (‘R.Y tracts’) are found in the highest excess. In prokaryotes, W tracts predominate (A,T ‘rich’). A pre-program, ANEX, parses database annotation files of GenBank and EMBL, to produce a convenient one-line list of every gene (exon, intron) in a genome. The main unit lists and analyzes tracts of the three possible binary pairs (R.Y, K.M and S;W). As an example, the results of R.Y tract mapping of mammalian gene p53 is described.


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