PFAMSCOP {PFAM.db} | R Documentation |
This is an R object that always contains mappings from a PFAM accession (AC) to a SCOP ID
The SCOP ID along with the start point and end point have been attached to the PFAM accessions 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 PFAM to SCOP: x <- PFAMSCOP # Get the PFAM identifiers that are mapped to a SCOP mapped_keys <- mappedkeys(x) # Convert to a list xx <- as.list(x[mapped_keys]) if(length(xx) > 0) { # Get the SCOP info for the first five PFAM IDs xx[1:5] # Get the first one xx[[1]] }