An R Implementation of the 'Align-GVGD' Method
Convert an alignment position to residue position
Pipe operator
Converts a sequence profile to an alignment
agvgd: An R Implementation of the 'Align-GVGD' Method
Align-GVGD (A-GVGD)
Pre-bundled alignments
The 20 standard amino acids
Determine CPV ranges
Deviation function
Grantham deviation
Grantham variation
Read in AGVGD Web Results
Read a protein sequence multiple alignment
Read a file with amino acid substitutions
Convert a residue position to an alignment position
Chop a string into sub-strings of fixed width
Export an alignment to FASTA
Generate and export a list of substitutions
'Align-GVGD' ('A-GVGD') is a method to predict the impact of 'missense' substitutions based on the properties of amino acid side chains and protein multiple sequence alignments <doi:10.1136/jmg.2005.033878>. 'A-GVGD' is an extension of the original 'Grantham' distance to multiple sequence alignments. This package provides an alternative R implementation to the web version found on <http://agvgd.hci.utah.edu/>.
Useful links