SubVis: an interactive R package for exploring the effects of multiple substitution matrices on pairwise sequence...

Area of Science:

• Bioinformatics
• Computational Biology
• Protein Science

Background:

• Protein mutations, involving amino acid substitutions, are key to biological understanding.
• Substitution matrices (e.g., BLOSUM, PAM) model these changes for sequence alignment.
• Current tools lack efficient methods for comparing multiple matrices, hindering optimal alignment.

Purpose of the Study:

• To introduce SubVis, an interactive R package for applying and comparing multiple substitution matrices.
• To enable simultaneous exploration of pairwise alignments using various matrices.
• To facilitate the selection of suitable matrices for specific research hypotheses.

Main Methods:

• Developed an R package, SubVis, integrating alignment functions from R.
• Utilized the Shiny platform for interactive parameter modification.
• Implemented JavaScript for dynamic visualizations of alignment quality and substitutions.

Main Results:

• SubVis allows simultaneous loading and application of multiple predefined and custom substitution matrices.
• Interactive visualizations provide insights into high-level and low-level alignment details.
• The package streamlines the comparison of matrix effects on pairwise alignments.

Conclusions:

• SubVis offers a novel solution for interactive comparison of protein substitution matrices.
• The tool enhances the process of selecting appropriate matrices for accurate sequence alignment.
• SubVis empowers researchers to model specific hypotheses and improve alignment quality.