Convert GenBank Nocleotide Accession to Gene Symbols

Question

[minoo]

Hi,

I'm want to convert a list of GenBank Nocleotide Accession to gene symbols. I tried to use bioDBnet: db2db to convert but It wasn't a good idea because my list is too great. Any better idea?

I would be really grateful.

[Benn]

I would use biomart in R.

[524129693]

Hello, I have the same question. Can you help me? You can give a short example? I have a list genbank accession number, my data is lncRNA genebank ID.e.g:AJ001495,AF339794,AK127588,BC039327,BC035392,NR_033244.1,BC038766,CR608805,S81294.

    ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
 values=c("AJ001495","AF339794","AK127588,"BC039327","BC035392","NR_033244","BC038766","CR608805","S81294")
    dat=getBM(attributes=c("protein_id","embl","hgnc_symbol"),filters="protein_id",values=values, mart=ensembl)
    dat
    protein_id  embl        hgnc_symbol
    <0 rows> (or 0-length row.names)

I know that the "filters" is wrong, But I do not know how to choose the "filters" for my data. The "biomart" package does not have "genbank accession" databaes. Look forward to your reply!

[Amirhossein Hajianpour]

use biomaRt, but if you want a detailed info, you can also download the original annotation table for example from here:
http://www.affymetrix.com/estore/browse/level_three_category_and_children.jsp;jsessionid=D72602AAA897609E79C2358F26C1C7AE.prd11com?fromBreadCrumb=true&expand=true&parent=35617&navAction=pop&category=35871
open it with excel and look for them one-by-one.

[Malcolm.Cook]

care to provide a short example of exact Input/Output you would expect?