TRF

TRF identifies tandem repeats in DNA sequences to detect and characterize contiguous approximate copies of nucleotide patterns for analysis of genomic repeat structure and variation.

Key Features:

• Pattern and Size Independence: Does not require prior knowledge of the repeat pattern or its size.
• K-tuple Matching Methodology: Uses k-tuple matching to identify tandem repeats, avoiding full-scale alignment matrix computations.
• Detection of Mutational Variants: Models repeats by assessing percent identity and the frequency of insertions or deletions (indels) between adjacent copies and applies statistically based recognition criteria to detect extensively mutated repeats.
• Versatility in Repeat Size Detection: Places no restriction on repeat size and has been applied to sequences ranging from a few kilobases up to several hundred kilobases (reported analyses 3 kb–700 kb).

Scientific Applications:

• Human frataxin gene: Identification and analysis of tandem repeats within the human frataxin gene.
• Human beta T cell receptor locus: Detection of tandem repeats in the human beta T cell receptor locus sequence.
• Yeast chromosomes: Analysis of tandem repeats across two yeast chromosomes.

Methodology:

Employs k-tuple matching combined with statistical recognition criteria based on percent identity and indel frequency between adjacent pattern copies.