FORUMCategory: BioinformaticsGene ID Conversion
jrosner Staff asked 4 years ago



I need to perform a number of gene ID conversions, for e.g. Entrez to RefSeq, RefSeq to gene symbol, and others.
Can anyone suggest what is the best Gene Id conversion tool?

2 Answers
Best Answer
jstafford answered 4 years ago



biomaRt all the way! https://bioconductor.org/packages/release/bioc/html/biomaRt.html
If you don’t like using R, they have a web interface here: http://www.biomart.org/

jrosner Staff replied 4 years ago

What about DAVID? Someone recommended that to me, but i wasn’t sure. Are there advantages of Entrez over DAVID?

jstafford replied 4 years ago

DAVID looks actually fairly useful if all you want to do is convert gene IDs (full confession… never used it yet myself). I think the main advantage of Biomart is that it can not only fetch/convert gene IDs, but also can be used to retrieve other types of annotations at the same time (GO terms, orthologs, gene sequences, etc.). So instead of having to learn multiple tools for converting/retrieving annotation, you can use Biomart and do almost everything with just one tool.

But hey, if DAVID works well, go for it! (as long as the job gets done, right?)

zhibin Staff answered 4 years ago



You can try DAVID (https://david.ncifcrf.gov/conversion.jsp) and bioDBnet (https://biodbnet-abcc.ncifcrf.gov/db/db2db.php)