\name{@ANNOBJPREFIX@CAZY2AC}
\alias{@ANNOBJPREFIX@CAZY2AC}
\alias{@ANNOBJPREFIX@DE2AC}
\alias{@ANNOBJPREFIX@ID2AC}
\alias{@ANNOBJPREFIX@HOMSTRAD2AC}
\alias{@ANNOBJPREFIX@INTERPRO2AC}
\alias{@ANNOBJPREFIX@LOAD2AC}
\alias{@ANNOBJPREFIX@MEROPS2AC}
\alias{@ANNOBJPREFIX@MIM2AC}
\alias{@ANNOBJPREFIX@PRINTS2AC}
\alias{@ANNOBJPREFIX@PROSITE2AC}
\alias{@ANNOBJPREFIX@PROSITEPROFILE2AC}
\alias{@ANNOBJPREFIX@RM2AC}
\alias{@ANNOBJPREFIX@SMART2AC}
\alias{@ANNOBJPREFIX@TC2AC}
\alias{@ANNOBJPREFIX@TP2AC}
\alias{@ANNOBJPREFIX@URL2AC}
\title{Mappings from an ID to a PFAM Accession number}
\description{
This is an R object that contains mapppings from an ID to its
PFAM Accession number (AC)
}
\details{
For each of the aliases listed above, there is a mapping object that
corresponds which will map you from the ID type in the environments
name to the appropriate PFAM accession number. So for example
@ANNOBJPREFIX@CAZY2AC will map from CAZY IDs to PFAM IDs while
@ANNOBJPREFIX@DE2AC will map from Descriptions to PFAM IDs.
Details on supported things that are mapped to:
CAZY: The CAZy database ()
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, ) 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.
LOAD: LOAD ID for all the Accession number in the database.
MEROPS: The MEROPS database () 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, ) 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: McKusick, V.A.: Mendelian
Inheritance in Man. A Catalog of Human Genes and Genetic
Disorders. Baltimore: Johns Hopkins University Press, 1998 (12th
edition). 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
PRINTS: PRINTS ()
is a compendium of protein fingerprints.
PROSITEPROFILE: A list of associated PROSITE PROFILE ID.
RM: Reference Medline ()
SMART: SMART (a Simple Modular Architecture Research Tool, ) 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.
}
\references{\url{http://www.sanger.ac.uk/Software/Pfam/} and
\url{ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/userman.txt}}
\examples{
#To map from CAZY to PFAM IDs:
x <- @ANNOBJPREFIX@CAZY2AC
# Get the CAZY 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 PFAM ID for the first five CAZYs
xx[1:5]
# Get the first one
xx[[1]]
}
#Or to use the DE2AC mapping:
x <- @ANNOBJPREFIX@DE2AC
# Get the Descriptions 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 PFAM ID for the first five DEs
xx[1:5]
# Get the first one
xx[[1]]
}
#etc.
}
\keyword{datasets}