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.
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.
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.
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The problem with
BiomaRtis 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.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.