Question: How should a query a gene type in multiple genomes?
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gravatar for elsoja
13 months ago by
elsoja30
elsoja30 wrote:

I want to query all genes of a specific type (eg.: microRNAs) in genomes of multiple species. Initially I was doing this using Ensemble's BioMart, but it limits me to query a single genome at a time and I the web interface makes it impossible to automate the process. Is there a better way of doing this task?

Thank you.

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ADD COMMENTlink modified 13 months ago by genomax67k • written 13 months ago by elsoja30
1
gravatar for JJ
13 months ago by
JJ430
JJ430 wrote:

With query you mean what exactly? What do you want to get?

However, try the R package BiomaRt - this should allow you to automate the process. Alternatively download the gff / gtf files of all the species from Ensembl and do it in bash by selecting the biotype.

ADD COMMENTlink modified 13 months ago • written 13 months ago by JJ430

The problem with BiomaRt is that I can only query one database (in this case, one genome) at a time. I suppose I could create a loop to automatequerying though multiple databases.

ADD REPLYlink modified 13 months ago • written 13 months ago by elsoja30
1

Yes, that's true but I cannot think of an approach where you can select multiple species at the same time. I personally would prefer using bash (e.g., grep) and selecting certain biotypes from all the gtf/gff files - this could be neatly automated.

ADD REPLYlink written 13 months ago by JJ430
0
gravatar for genomax
13 months ago by
genomax67k
United States
genomax67k wrote:

Use RNA central for things related to RNA. Example query for microRNA. Limit by selecting species in left column. There is an API available.

For other types of data NCBI's eUtils or Ensembl API would be the way to go.

ADD COMMENTlink modified 13 months ago • written 13 months ago by genomax67k

I didn't know about RNA Central. I'll look into it right now. Thank you!

As far as I know, it's not possible to query a specific gene type in Entrez, but I'll investigate it.

ADD REPLYlink written 13 months ago by elsoja30

Can you post an example of gene type you would look for?

ADD REPLYlink written 13 months ago by genomax67k
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