PFAMCAZY               package:PFAM.db               R Documentation

_M_a_p_p_i_n_g_s _f_r_o_m _a _P_F_A_M _A_c_c_e_s_s_i_o_n _n_u_m_b_e_r _t_o _a_n_o_t_h_e_r _k_i_n_d _o_f _I_D

_D_e_s_c_r_i_p_t_i_o_n:

     This is an R object that always contains mappings from a PFAM ID
     to the other ID type named by the object

_D_e_t_a_i_l_s:

     For each of the aliases listed above, there is a mapping object
     that corresponds which will map you from the appropriate PFAM
     accession number to the ID type that is in the environments name. 
     So for example PFAMCAZY will map from PFAM IDs to CAZY IDs while
     PFAMDE will map from PFAM IDs to Descriptions.

     CAZY: The CAZy database (<URL: http://afmb.cnrs-mrs.fr/CAZY/>)
     describes the families of structurally-related catalytic and
     carbohydrate-binding modules (or functional domains) of enzymes
     that degrade, modify, or create glycosidic bonds.

     DE:  Definition for all the Accession number in the database.

     ID:  Associated Identification for all the Accession number in the
     database.

     HOMSTRAD:  HOMSTRAD (HOMologous STRucture Alignment Database,
     <URL: http://www-cryst.bioc.cam.ac.uk/homstrad/>) is a curated
     database of structure-based alignments for homologous protein
     families. Reference: Mizuguchi K, Deane CM, Blundell TL,
     Overington JP. (1998) HOMSTRAD: a database of protein structure
     alignments for homologous families. Protein Science 7:2469-2471.

     INTERPRO:  Associated INTERPRO ID for all the Accession number in
     the database.  <URL: http://www.ebi.ac.uk/interpro/> 

     LOAD:  LOAD ID for all the Accession number in the database.

     MEROPS:  The MEROPS database (<URL: http://merops.sanger.ac.uk/>)
     is an information resource for peptidases (also termed proteases,
     proteinases and proteolytic enzymes) and the proteins that inhibit
     them. Reference: Rawlings, N.D., Tolle, D.P. & Barrett, A.J.
     (2004) MEROPS: the peptidase database. Nucleic Acids Res. 32
     Database issue, D160-D164

     MIM:  MIM (a.k.a. OMIM, <URL: http://www.ncbi.nlm.nih.gov/omim/>)
     is a catalog of human genes and genetic disorders authored and
     edited by Dr. Victor A. McKusick and his colleagues at Johns
     Hopkins and elsewhere. Reference:  <MIM> MIM: McKusick, V.A.:
     Mendelian Inheritance in Man. A Catalog of Human Genes and Genetic
     Disorders. Baltimore: Johns Hopkins University Press, 1998 (12th
     edition). <OMIM> Online Mendelian Inheritance in Man, OMIM (TM).
     McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins
     University (Baltimore, MD) and National Center for Biotechnology
     Information, National Library of Medicine (Bethesda, MD), 2000

     PFAMB:  Pfam-B is an automatic clustering of the rest of SWISSPROT
     and TrEMBL derived from the PRODOM database.

     PRINTS:  PRINTS (<URL:
     http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/>) is a compendium of
     protein fingerprints.

     PROSITEPROFILE:  A list of associated PROSITE PROFILE ID.

     RM:  Reference Medline (<URL:
     http://www.ncbi.nlm.nih.gov/PubMed/>)

     SMART:  SMART (a Simple Modular Architecture Research Tool, <URL:
     http://smart.embl-heidelberg.de/>) allows the identification and
     annotation of genetically mobile domains and the analysis of
     domain architectures.  Reference: (1) Schultz et al. (1998) Proc.
     Natl. Acad. Sci. USA 95, 5857-5864.  (2) Letunic et al. (2004)
     Nucleic Acids Res 32, D142-D144

     TC:  Trusted cutoff for all the Accession number in the database.

     TP:  A list of associated Type field for the given Accession.

     URL:  A list of associated URL for all the Accession number in the
     database.

_R_e_f_e_r_e_n_c_e_s:

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

_E_x_a_m_p_l_e_s:

             #To map from PFAM to CAZYs:
             x <- PFAMCAZY
             # Get the PFAM identifiers that are mapped to a CAZY
             mapped_keys <- mappedkeys(x)
             # Convert to a list
             xx <- as.list(x[mapped_keys])
             if(length(xx) > 0) {
               # Get the CAZY for the first five PFAM IDs
               xx[1:5]
               # Get the first one
               xx[[1]]
             }

             #Or to use the DE mapping:
             x <- PFAMDE
             # Get the PFAM identifiers that are mapped to a DE
             mapped_keys <- mappedkeys(x)
             # Convert to a list
             xx <- as.list(x[mapped_keys])
             if(length(xx) > 0) {
               # Get the DE for the first five PFAM IDs
               xx[1:5]
               # Get the first one
               xx[[1]]
             }

             #etc.

