REP2

REP2 detects and analyzes tandem repeats (TRs) in protein sequences using curated profiles and specific thresholds to identify 11 common TRs and support studies of their structural and evolutionary roles.

Key Features:

• Detection of tandem repeats (TRs): Identification and analysis of short, contiguous amino-acid segments that repeat within protein sequences.
• Curated profiles and specific thresholds: Use of curated profiles and tailored score thresholds to improve repeat identification accuracy.
• Identification of 11 common TRs: Explicit targeting of 11 common tandem repeats for sensitive detection.
• Support for individual and aligned sequences: Analysis capabilities apply to both single protein sequences and aligned protein sequence sets.
• Precomputed reference proteomes: Includes precomputed analyses for 78 UniProt reference proteomes to provide reference annotations.
• Robustness to sequence divergence: Methodology addresses the rapid divergence of TRs that limits classical sequence-comparison algorithms.

Scientific Applications:

• Protein structure and function: Characterization of repeat-derived domains to investigate their contributions to protein structure and function.
• Protein interactions: Analysis of repetitive domains that mediate or modulate protein–protein interactions.
• Comparative genomics and evolution: Comparative-genomics studies of the evolutionary dynamics of tandem repeats across species using reference proteomes.
• Molecular biology and genetics: Application to molecular biology and genetics research focused on repeat-associated variation and function.

Methodology:

REP2 applies curated profiles with specific score thresholds to detect 11 common tandem repeats in protein sequences, supports analysis of individual and aligned protein sequences, and provides precomputed annotations for 78 UniProt reference proteomes to mitigate sensitivity loss from classical sequence-comparison algorithms due to rapid TR divergence.