Conversion of Amino Acids into Integer Values
A sequence containing standard amino acids is converted into a sequence of integer values. An offset for the code can be specified.
string vector containing a sequence of standard amino acids
offset, added to the specified code
integer vector of the values to be assigned to the amino acids
logical, if TRUE the specific encoding is printed
The default values for the code are the integer values in the range 0 to 19. It is possible to use another numerical code for the 20 amino acids. The default coding order of the amino acids is:
CYS, MET, PHE, ILE, LEU, VAL, TRP, TYR, ALA, GLY, THR, SER, ASN, GLN, ASP, GLU, HIS, ARG, LYS, PRO. Each amino acid is converted to a single element according to the
code-vector. The offset
offset is added. Both sequences with three-letter and one-letter code can be handled.
Returns a sequence of integer values according to the given numerical code.
The function assigns values only for the standard amino acids. This function includes source code of the bio3d package.
Grant, Rodrigues, ElSawy, McCammon, Caves, (2006) Bioinformatics 22, 2695–2696.