PFAMSCOP2AC {PFAM.db}R Documentation

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

Examples


        #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]]
        }


[Package PFAM.db version 2.2.0 Index]