agvgd0.1.2 package

An R Implementation of the 'Align-GVGD' Method

poi_to_res

Convert an alignment position to residue position

pipe

Pipe operator

profile_to_alignment

Converts a sequence profile to an alignment

agvgd-package

agvgd: An R Implementation of the 'Align-GVGD' Method

agvgd

Align-GVGD (A-GVGD)

alignment_file

Pre-bundled alignments

amino_acids

The 20 standard amino acids

cpv_ranges

Determine CPV ranges

dev

Deviation function

gd

Grantham deviation

gv

Grantham variation

read_agvgdweb_results

Read in AGVGD Web Results

read_alignment

Read a protein sequence multiple alignment

read_substitutions

Read a file with amino acid substitutions

res_to_poi

Convert a residue position to an alignment position

str_chop

Chop a string into sub-strings of fixed width

write_alignment

Export an alignment to FASTA

write_substitutions

Generate and export a list of substitutions

Download source packageRead PDF manual

'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/>.

  • Maintainer: Ramiro Magno
  • License: MIT + file LICENSE
  • Last published: 2022-09-10

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