Convert Between 1-letter and 3-letter Aminoacid Codes
Convert between one-letter IUPAC aminoacid codes and three-letter PDB style aminoacid codes.
aa123(aa) aa321(aa)
aa |
a character vector of individual aminoacid codes. |
Standard conversions will map ‘A’ to ‘ALA’, ‘G’ to
‘GLY’, etc.
Non-standard codes in aa will generate a warning and return
‘UNK’ or ‘X’.
A character vector of aminoacid codes.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
For a description of IUPAC one-letter codes see:
http://www.insdc.org/documents/feature_table.html#7.4.3
For more information on PDB residue codes see:
http://ligand-expo.rcsb.org/ld-search.html
# Simple conversion
aa123(c("D","L","A","G","S","H"))
aa321(c("ASP", "LEU", "ALA", "GLY", "SER", "HIS"))
## Not run:
# Extract sequence from a PDB file's ATOM and SEQRES cards
pdb <- read.pdb("1BG2")
s <- aa321(pdb$seqres) # SEQRES
a <- aa321(pdb$atom[pdb$calpha,"resid"]) # ATOM
# Write both sequences to a fasta file
write.fasta(alignment=seqbind(s,a), id=c("seqres","atom"), file="eg2.fa")
# Alternative approach for ATOM sequence extraction
pdbseq(pdb)
pdbseq(pdb, aa1=FALSE )
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.