PFAMSCOP2AC {PFAM.db} | R Documentation |
This is an R object that always contains mappings from a SCOP ID to a PFAM accession (AC)
The PFAM accession number has been attached to the SCOP IDs in this object.
More Details: Structural Classification of Proteins (http://scop.mrc-lmb.cam.ac.uk/scop/index.html). Reference: Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540
http://www.sanger.ac.uk/Software/Pfam/ and ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/userman.txt
#To map from SCOP to PFAM IDs: x <- PFAMSCOP2AC # Get the SCOP identifiers that are mapped to a PFAM ID mapped_keys <- mappedkeys(x) # Convert to a list xx <- as.list(x[mapped_keys]) if(length(xx) > 0) { # Get the SCOP ID for the first five CAZYs xx[1:5] # Get the first one xx[[1]] }