ID conversion tool: from RefSeq mRNA accessions to GO-biological process

Question

[j-blanchard]

Hi everyone,

I am studying genes under positive selection in several lines. I would like to cluster genes under positive selection by biological process. I have the RefSeq mRNA accessions and I would like to access to the corresponding GO-biological process.

I found a website resource which do exactly what I want (bioDBnet). Nevertheless, I would like to introduce the id conversion in a pipeline in order to do the clustering automatically. As a consequence, I need either a id conversion tool or a list of corresponding ID "RefSeq mRNA accessions <->GO terms".

If anyone knows where I can find something like this, I will be very grateful.

Answer 1

[Dr Reema Singh]

See this How Do I Do Simple Go Term Lookup Given A Gene (Or Mrna) Identifier?. Also, try GO.db bioconductor package

[j-blanchard]

Thanks a lot, I didn't find that post. The biomaRt packages works well for what I want.

Answer 2

[j-blanchard]

If anyone is interested, I also find these conversion tables which were very useful for me : dbOrg