Mappings from a SCOP ID to a PFAM Accession number

Description

This is an R object that always contains mappings from a SCOP ID to a PFAM accession (AC)

Details

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

References

http://www.sanger.ac.uk/Software/Pfam/ and ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/userman.txt

See Also

• AnnotationDb-class for use of the select() interface.

Examples

## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.

## Bimap interface:
#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]]
}