AAstretch

AAstretch identifies and extracts imperfect homopolymeric amino acid repeats from protein sequences and their corresponding coding sequences—focusing on glutamine (polyQ) stretches—to characterize residue context and polyQ-associated genetic features relevant to neurodegenerative disease research.

Key Features:

• Implementation: Implemented as a suite of Perl scripts that process protein sequences and their corresponding coding sequences.
• Customizable Search Parameters: Allows user-defined target amino acids, maximal repeat length, and permissible insertion proportions for repeat detection.
• Proteome-wide Repeat Detection: Scans entire proteomes to identify and extract imperfect homopolymeric repeats, including polyQ stretches.
• Insertion and Flanking Residue Assessment: Evaluates insertions within repeats and characterizes the nature of residues flanking homopolymeric stretches.
• Residue Bias and Comparative Analysis: Detects amino acid residue biases associated with polyQs across multiple eukaryotic proteomes and highlights over- and under-representation patterns (e.g., Pro, Leu, His versus Asp, Cys, Gly).

Scientific Applications:

• Neurodegenerative Disease Research: Characterizes genetic and protein sequence contexts of polyQ expansions relevant to diseases such as Huntington's disease and spinocerebellar ataxias.
• Evolutionary Biology: Investigates co‑evolution and selective pressures on residues surrounding polyQ tracts across diverse eukaryotic proteomes.

Methodology:

Operates as a suite of Perl scripts that scan proteomes and coding sequences using user-defined parameters to identify and extract imperfect homopolymeric repeats, assess insertions and flanking residues, and compile residue-bias analyses for evolutionary context.