PR2ALIGN

PR2ALIGN aligns protein sequences using customizable weighted biochemical-property scoring functions to compute optimal minimal-distance global alignments for analyses of protein structure-function relationships and evolutionary comparisons.

Key Features:

• Customizable Alignment Scoring Functions: Allows definition of flexible scoring functions using weighted biochemical properties of amino acids instead of static substitution matrices.
• Biochemical Property Profiles: Compares profiles of biochemical properties between sequences and accepts any number of amino acid properties with user-assigned weights.
• Optimal Minimal Distance Global Alignment: Computes global alignments by minimizing distances between aligned residues based on user-specified weighted biochemical property profiles.
• User-Specific Flexibility: Enables alignment tailored to specific scientific hypotheses by varying included biochemical properties and their weights.

Scientific Applications:

• Computational molecular biology: Facilitates analyses that require alignments sensitive to biochemical characteristics of amino acids.
• Protein structure-function studies: Supports investigations of sequence features that influence protein structure and functional residues.
• Evolutionary biology: Assists comparative and evolutionary analyses where biochemical context affects inference of homology.
• Context-dependent sequence analysis: Applies to domains where the biochemical context of amino acids significantly influences biological interpretation.

Methodology:

Users specify a set of biochemical properties for amino acids; assign weights to these properties; and calculate distances between aligned residues based on these weighted property profiles to obtain an optimal minimal-distance global alignment.