REPPER

REPPER: Fourier Transform and Self-Alignment Analysis of Protein Repeats

REPPER detects periodicities and internal repeats in protein sequences using Fourier Transform-based analysis and self-alignment strategies to identify short gapless repeats and repetitive structural motifs.

Key Features:

• FTwin (Fourier Transform-based Analysis): Applies Fourier Transform to protein sequences after assigning numerical values to amino acids based on physicochemical properties such as hydrophobicity, enabling detection of periodic patterns in the frequency domain.
• REPwin (Repeat-based Analysis): Performs self-alignments to identify and display significant internal similarities and repeat regions within protein sequences.
• Sliding Window Technique: Uses sliding window analysis in FTwin and REPwin to independently detect distinct periodic regions within the same protein sequence, improving sensitivity and specificity.
• Complementary Predictive Tools: Integrates secondary structure prediction (PSIPRED) and coiled coil prediction (COILS) to support structural interpretation of repetitive regions.

Scientific Applications:

• Protein Structure Analysis: Identifies short gapless repeats and periodicities to characterize structural organization and functional domains.
• Fibrous Protein Research: Analyzes repetitive motifs and coiled coil regions relevant to fibrous protein stability and architecture.
• Functional Annotation: Detects repeat regions associated with protein–protein interactions, aggregation properties, and domain architecture.

Methodology:

REPPER combines Fourier Transform-based frequency analysis of numerically encoded amino acid sequences with self-alignment-based repeat detection, applying a sliding window framework to resolve multiple periodic regions within individual proteins.