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How I get mRNA accession no if I have gene name and location with the help of perl

Hi,

I have a list of Gene Names with mRNA location. I want to know the mRNA Accession no for the particular location in GenBank file. I know it is easy to retrieve from NCBI one by one. But I have a big list so I want to retrieve in short time. If you have any solution like script etc please help me in this regard.

Best

Anshul

mrna mirna perl parsing
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updated by Russ Russ • written by georgians • georgians

I have a list of Gene Names with mRNA location. I want to know the mRNA Accession no for the particular location in GenBank file.

it's not clear to me. Show an example please.

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written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

If I understand your question correctly, you should be able to use BioMart on Ensembl:

  1. Select the "Ensembl Genes 90" database and then choose your organism (provided it is in Ensembl).
  2. In the sidebar, select "Filters".
  3. In the main window, expand the "GENE" box and select "Input external references ID list".
  4. From the dropdown menu select "Gene names" and paste your list of gene names.
  5. In the sidebar, select "Attributes"
  6. Expand the "External" box Select "RefSeq mRNA ID"
  7. Hit the results button
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written by Russ Russ

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