RefseqID to gene symbol for multiple species

Question

[Jacob]

Hi all,

I'm a little stuck on a refseq conversion question. Im looking to convert the Refseq identifiers i get from a blast search to a gene symbol, so i can just identify one match per gene. If it was just human, i could use the Refseq_curated database, but I am searching in all mammals.

I have also tried BioDBnet, however it seems to be retrieving the wrong gene symbols for more obscure species.

I have had a crack at using Entrez Direct, but cant seem to return the Refseq ID and gene at the same time?

Any assistance would be much appreciated.

[ATpoint]

Please add anything to illustrate the problem. Like identifiers, code, anything.

Answer 1

[vkkodali_ncbi]

You can do this using NCBI Datasets. Specifically, go to https://ncbi.nlm.nih.gov/datasets/gene/ and use the "Upload a text file" tab to load a list of RefSeq accessions. The output table has Gene identifiers as well as a column named "Input" with the RefSeq accession from the uploaded file. You can download that table as TSV and work with it.

NCBI Datasets has a command line interface if you want to do this on the command line. EntrezDirect is an option too, if you prefer that way.

[Jacob]

NCBI Datasets was the way to go. I did have to use the command line interface though, the web version does not include the query when you download the table.

Thank you for your help.