Repetita

Repetita: Detection of Solenoid Repeats in Protein Sequences

Repetita detects solenoid repeats in protein sequences, including cases where repeat periodicity is obscured at the primary sequence level, by analyzing numerical functions derived from amino acid properties.

Key Features:

• Amino Acid Property Encoding: Integrates five numerical functions based on polarity, secondary structure propensity, molecular volume, codon diversity, and electric charge.
• Discrete Fourier Transform Analysis: Applies Discrete Fourier Transform (DFT) to generate spectra that reveal repeat periodicity and accurately estimate repeat lengths.
• Phase Space Classification: Uses a phase space parameterized by two quantities derived from Fourier spectra to distinguish non-homologous globular proteins from solenoid repeat-containing proteins.

Scientific Applications:

• Structural and Evolutionary Analysis: Identifies solenoid repeats to support structural characterization, functional annotation, and analysis of accelerated evolution in repeat-containing proteins.

Methodology:

Protein sequences are transformed into five numerical profiles based on defined amino acid properties. Discrete Fourier Transform (DFT) is applied to candidate repeat-coding regions to produce frequency spectra. Spectral features indicative of periodicity are extracted, and two derived spectral parameters define a phase space used to classify proteins and determine repeat periodicity and length.