\name{AnnotationFuncs-package}
\title{Annotation translation functions}
\description{\tabular{ll}{
Package:  \tab  AnnotationFuncs\cr
Type:  \tab  Package\cr
Version:  \tab  1.3.0\cr
Date:  \tab  2011-06-10\cr
License:  \tab  GPL-2\cr
LazyLoad:  \tab  yes\cr
}}
\details{Functions for handling translations between different identifieres using
the Biocore Data Team data-packages (e.g. \code{org.Bt.eg.db}).  
Primary functions are \code{\link{translate}} for translating
and \code{\link{getOrthologs}} for efficient lookup of homologes 
using the Inparanoid databases.
Other functions include functions for selecting Refseqs or Gene Ontologies (GO).}
\alias{AnnotationFuncs}
\docType{package}
\author{Stefan McKinnon Edwards  \email{stefan.hoj-edwards@agrsci.dk}}
\references{\url{http://www.iysik.com/index.php?page=annotation-functions}}
\keyword{package}
\seealso{\code{\link{translate}}, \code{\link{getOrthologs}}}
\examples{library(org.Bt.eg.db)
gene.symbols <- c('DRBP1','SERPINA1','FAKE','BLABLA')
# Find entrez identifiers of these genes.
eg <- translate(gene.symbols, org.Bt.egSYMBOL2EG)
# Note that not all symbols were translated.

# Go directly to Refseq identifiers.
refseq <- translate(gene.symbols, from=org.Bt.egSYMBOL2EG, to=org.Bt.egREFSEQ)
# Pick the proteins:
pickRefSeq(refseq, priorities=c('NP','XP'), reduce='all')}