Gene And Transcript Id Conversion · Biostar

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Gene And Transcript Id Conversion

Hi All,

So I'm trying to basically get a list of all Entrezgenes and their corresponding gene names, and transcript ids. I've tried biomart ensembl and UCSC genome browser but had no luck with either. Ensembl gives me lots of missing rows of data, and ucsc doesn't appear to offer any entrez ids at all. Anyone know where I could download, or query a table of all entrezgenes?

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updated 14.1 years ago by Pierre Lindenbaum

• written 14.1 years ago by Davy

1 answer

All the information you're looking is available under: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/

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written 14.1 years ago by Pierre Lindenbaum

Excuse my ignorance, but any suggestions for the best way to deal with these files? I was looking into parsing them with python, but that seems very DIY for something that should be relatively routine.

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written 14.1 years ago by Davy

I would use the ASN1 files, convert it to XML using asn2xml ( http://www.ncbi.nlm.nih.gov/IEB/ToolBox/XML/ncbixml.txt ) and parse it with a (python-based) sax parser

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written 14.1 years ago by Pierre Lindenbaum

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