TRACTS

TRACTS identifies and analyzes binary DNA tracts—contiguous stretches composed exclusively of two specific bases, such as purines-pyrimidines (R.Y), adenine-thymine-guanine-cytosine (K.M), or cytosine-guanine-adenine-thymine (S.W)—in genomic sequences to map their locations, frequencies, and length distributions for studies of genome structure and function.

Key Features:

• Binary tract detection: Detects and enumerates contiguous stretches composed exclusively of two bases for the R.Y, K.M, and S.W binary pairs.
• Positional mapping and quantification: Maps genomic positions of tracts and computes their frequencies and length distributions.
• Annotation integration via ANEX: Integrates with ANEX to process GenBank and EMBL annotation files and generate lists of genes with exon and intron regions.
• Output reporting: Produces detailed outputs including positional information and length-distribution summaries for each identified tract.

Scientific Applications:

• Correlation with gene annotation: Correlates binary tract locations with exon and intron annotations derived from GenBank and EMBL files.
• Genome structure and function studies: Enables investigation of the potential roles of long binary tracts in genetic regulation and genome stability.
• Comparative genomics: Facilitates assessment of tract prevalence across taxa, noting oligopurine-oligopyrimidine (R.Y) tracts predominate in eukaryotes and adenine-thymine rich (W) tracts often predominate in prokaryotes.
• Gene-specific analysis: Supports focused analyses such as the documented application to the mammalian p53 gene.

Methodology:

Lists and analyzes tracts of three binary pairs (R.Y, K.M, S.W), outputs positional information and length distributions, and uses ANEX to process GenBank and EMBL annotation files to produce gene lists including exon and intron regions.