TRAP

TRAP analyzes tandemly repeated DNA sequences to select, classify, quantify, and annotate satellite and other tandem repeats for genomic analyses.

Key Features:

• Implementation: Implemented as a Perl program.
• Unified analysis framework: Consolidates multiple analyses related to tandem repeats into a single workflow.
• Integration with Tandem Repeats Finder (TRF): Processes outputs from Tandem Repeats Finder (TRF) to detect and characterize tandem repeats.
• Global analysis of satellite DNA content: Performs genome-wide assessment of the distribution and abundance of satellite and other tandem repeats.
• Data output formats: Generates results in HTML and comma-separated values (CSV) formats.
• Automated annotation generation: Produces feature table and GFF (General Feature Format) annotation files.

Scientific Applications:

• Genomic Research: Characterizes the distribution, abundance, and structural roles of tandem repeats within genomes.
• Comparative Genomics: Compares tandem repeat content across species or strains to investigate evolutionary differences.
• Functional Genomics: Provides annotated tandem repeat information to support studies of gene regulation, chromosomal organization, and genome stability.

Methodology:

Implemented in Perl; parses Tandem Repeats Finder (TRF) outputs to perform global analyses of satellite/tandem repeat content and to generate HTML, CSV, feature table, and GFF files.