Introduction

TRACTS is a program designed to detect and analyze binary tracts in a DNA sequence. Binary DNA tracts are nucleotide base sequences composed of two nucleotide bases only. Six two-base compositions are possible, and can be organized in two pairs plus a semi pair:

·        oligopurine.oligopyrimidine or R.Y tracts;

·        Keto.imino - G,T on one strand, A,C on the complimentary one - or K.M tracts;

·        Strong (S, - G,C) or weak (W - A,T) tracts; together - S;W tracts.  

The R, Y, K, M, W and S letters are the IUBMB (International Union of Biochemistry and Molecular Biology) specified letters for binary base combinations. A dot (.) is the IUBMB convention for separating bases on complimentary strands. The comma is the IUBMB convention for mixed bases on the same strand  (e.g. GGTTTG). The semicolon is the IUBMB convention for separating autocomplimentary oligonucleotides (For dot, comma and semicolon see reference [1] in the IUBMB recommendation). R.Y and K.M tracts can be run jointly because usually these tracts distribute evenly between strands. S;W are better run separately, as the autocomplimentary Weak and Strong sequences tend to behave quite differently.  An option to run also the other members separately is planned.

The main input file to the program is an annotated sequence in flat DDBJ/EMBL/GenBank format. This input file can be of a gene, a clone, contig, scaffold, chromosome etc. The user can insert the annotation part and the sequence part separately, as detailed below. The user can choose between the “mRNA” and  “CDS” feature keys. In the last case, noncoding exons will be considered part of the intergenic region (i.e. UTR regions will not be identified) and is the preferred key when mRNA data are available. Several additional parameters and options to be described have to be entered.

The program performs the following operations:

• The program finds all binary tracts within any given sequence, lists them and calculates the frequencies of the tracts of particular lengths. The values obtained are compared with the frequencies expected in random DNA of the same length and composition.
• The program extracts from the annotation files the locations of exons, introns and other gene features. This part produces a list of the genes in the input sequence regions, with a one-line entry for every intron or exon in the gene. The data are utilized to calculate tract frequencies in the different genic subregions.
• The program produces an annotated sequence in which each every feature category (exon, intron etc.) has its specific color. Identified tracts beyond a specified length are indicated by bold coloration on a special background.