Hi Boris,

The select() function in AnnotationDbi can help you map between 
identifiers. See ?select

Load the org package for the appropriate organism,
     library(org.Hs.eg.db)

  Theses are the available keytypes in the org package and are the 
possible forms of your input.
 > keytypes(org.Hs.eg.db)
  [1] "ENTREZID"     "ACCNUM"       "ALIAS"        "CHR"          "ENZYME"
  [6] "MAP"          "OMIM"         "PATH"         "PMID"         "REFSEQ"
[11] "SYMBOL"       "UNIGENE"      "ENSEMBL"      "ENSEMBLPROT"  
"ENSEMBLTRANS"
[16] "UNIPROT"      "UCSCKG"       "GO"

These are the columns that can be returned from a call to select() and 
are the possible forms of output.
 > cols(org.Hs.eg.db)
  [1] "ENTREZID"     "ACCNUM"       "ALIAS"        "CHR"          "ENZYME"
  [6] "GENENAME"     "MAP"          "OMIM"         "PATH"         "PMID"
[11] "REFSEQ"       "SYMBOL"       "UNIGENE"      "CHRLOC"       
"CHRLOCEND"
[16] "PFAM"         "PROSITE"      "ENSEMBL"      "ENSEMBLPROT"  
"ENSEMBLTRANS"
[21] "UNIPROT"      "UCSCKG"       "GO"

The gene id's in the TxDb.Hsapiens.UCSC.hg19.knownGene pacakge are 
Entrez id's. This is shown in the 'Type of Gene ID' field,

 > txdb
TranscriptDb object:
| Db type: TranscriptDb
| Supporting package: GenomicFeatures
| Data source: UCSC
| Genome: hg19
| Genus and Species: Homo sapiens
| UCSC Table: knownGene
| Resource URL: http://genome.ucsc.edu/
| Type of Gene ID: Entrez Gene ID
| Full dataset: yes
| miRBase build ID: GRCh37
| transcript_nrow: 80922
| exon_nrow: 286852
| cds_nrow: 235842
| Db created by: GenomicFeatures package from Bioconductor
| Creation time: 2012-03-12 21:45:23 -0700 (Mon, 12 Mar 2012)
| GenomicFeatures version at creation time: 1.7.30
| RSQLite version at creation time: 0.11.1
| DBSCHEMAVERSION: 1.0

Create a map between your tx names and the Entrez gene id's.  It is 
possible that none or multiple gene id's will be associated with each 
transcript. You can use the transcripts accessor to get the 
transcript-gene relationship,
     library(TxDb.Hsapiens.UCSC.hg19.knownGene)
     txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
     tx <- transcripts(txdb, col=c("tx_name", "gene_id"))
     txnames <- values(tx)[["tx_name"]]
     geneid <- values(tx)[["gene_id"]]
     df <- DataFrame(tx_name=rep(txnames, elementLengths(geneid)), 
gene_id=unlist(geneid, use.names=FALSE))

Get the gene id's for transcripts of interest
     entrezid <- df$gene_id[df$tx_name %in% df$tx_name[1:3]]

Map the Entrez gene id's to various protein id's,
 > select(org.Hs.eg.db, keys=entrezid, cols=c("PMID", "PFAM",  
"ENSEMBLPROT", "UNIPROT"), keytype="ENTREZID")
    ENTREZID     PMID         IPI  PfamId     ENSEMBLPROT UNIPROT
1     79501 16710414 IPI00169105 PF00001 ENSP00000334393  Q8NH21
2     79501 16710414 IPI01010102 PF00001 ENSP00000334393  Q8NH21
3 100133331 16751776 <NA> <NA> <NA> <NA>
4 100132287 16751776 <NA> <NA> <NA> <NA>

If you are not working with the TxDb.Hsapiens.UCSC.hg19.knownGene 
annotation you may be starting with different identifiers (e.g.., the 
gene id's may not be Entrez). You may also want to check out the PFAM.db 
package,
     biocLite("PFAM.db")

Valerie

On 05/07/2012 01:14 PM, Zybaylov, Boris L wrote:
>
> Dear Valerie, Thank you for your answer!
>
> Using your script I got now the list of translated transcripts that 
> contain the amino acid patterns I am interested in.
>
> Here are their names:> names(cds_seqs[i])   [1] "uc001ack.2" 
> "uc001acv.3" "uc001adm.3" "uc001ado.3" "uc001adp.3" "uc001adq.3" 
> "uc001adr.3" "uc001aee.1" "uc001aef.1"  [10] "uc009vjz.1" "uc010nyj.1" 
> "uc001aer.4" "uc009vkz.1" "uc010nyz.2" "uc001aji.1" "uc009vle.1" 
> "uc001ajj.1" "uc001ajk.1"  [19] "uc001ajy.2"…
>
> The question now is how do I go from these names to conventional 
> protein names and (or) ENTREZ identifiers?
>
> Thank you very much for your help!
>
> Best regards,
>
> Boris
>
> Dr. Boris Zybaylov
> Instructor
> Department of Biochemistry and Molecular Biology
> University of Arkansas Medical Sciences
> Little Rock, AR
> 1-501-686-7254
>
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