IMPACT_S

IMPACT_S integrates and analyzes selection-pressure results from Codeml (PAML), Datamonkey, and TreeSAAP to identify and characterize natural selection on protein-coding genes and map selected sites to protein structure for evolutionary and biochemical inference.

Key Features:

• Integration and filtering of selection-analysis outputs: Integrates and filters results from Codeml (PAML), Datamonkey, and TreeSAAP to combine evidence of selection at codon sites.
• Identification of selection categories: Identifies codon sites classified as under positive, neutral, or negative selection based on combined outputs.
• 3D homology modeling (Swiss-Model): Interfaces with Swiss-Model to generate homology models for protein sequences of interest.
• 3D mapping of selected sites (Jmol): Automatically maps identified sites onto protein structures using Jmol to provide spatial context for substitutions.
• Phylogenetic analysis (PhyML): Supports phylogenetic reconstruction with PhyML for downstream selection inference.
• Sequence and tree visualization (Archaeopteryx): Provides sequence alignment and tree visualization using Archaeopteryx.
• Plotting (Gnuplot): Produces plots and graphical summaries of selection metrics using Gnuplot.
• PDB downloading: Retrieves structural files from the Protein Data Bank via an integrated PDB downloader.

Scientific Applications:

• Detection of adaptive evolution: Enables detection of adaptive (positive) and purifying (negative) selection at codon resolution in protein-coding genes.
• Functional and biochemical inference: Maps non-synonymous substitutions to structural models to infer potential biochemical and functional consequences of mutations.
• Comparative analyses across taxa: Facilitates large-scale comparative analyses of selection pressures across multiple taxa using combined evidence from multiple methods.
• Case study application: Applicable to targeted studies such as analyses of toxicoferan-reptilian Cysteine-rich Secretory Proteins (CRiSPs) to illustrate selection and structural impacts.

Methodology:

Integrates, filters, and combines outputs from Codeml (PAML), Datamonkey, and TreeSAAP; interfaces with Swiss-Model for homology model generation; maps sites onto structures with Jmol; and employs PhyML, Archaeopteryx, Gnuplot, and a PDB downloader for phylogenetic analysis, visualization, plotting, and structure retrieval.