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Convert GenBank Nocleotide Accession to Gene Symbols

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.

rna-seq gene
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updated by Ram Ram • written by minoo • minoo

I would use biomart in R.

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written by Benn Benn

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!

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written by 524129693 • 524129693

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

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written by Malcolm.Cook Malcolm.Cook

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