Ensembl stable gene ID to NCBI gene symbols conversion_Plants

Will anyone guide me how to covert Ensembl stable gene ID to NCBI gene symbols. I have a list of >1800 IDs

Hi @susheel_raina

Try the tool AnnotateMyIDs :slight_smile:

Thank you jennaj but my plant i.e Prunus dulcis (Almond) is not there.
Only Arabidopsis is there among the plants.
I also have the chromosomal coordinates i. e Chromosome No., start and end coordinates of these gene IDs.Is there any other way out.


Hi @susheel_raina

Ok, thanks for explaining. If you can find or extract or create a tabular file with the “from” identifier and the “to” identifier and get that into Galaxy, you can do this directly instead. Ensembl might host that kind of data.

Biomart used to be a good source. We don’t host that data source at the usegalaxy.org server anymore but the usegalaxy.eu server still does, so I would try that first.

If that doesn’t work, the EU server also hosts more related tools – search the tool panel with the keyword “ensembl”. You can copy files between servers quickly (move files unless your history is really small!). Transfer entire histories from one Galaxy server to another

I’m guessing that the GTF you are using does not contain the “to” identifiers, which would be needed to do that comparison with coordinates. Same for a BED dataset. If both identifiers are not in a single file, there isn’t any information to match/replace.

Please see Data Manipulation Olympics

Hope that helps!