Hello, I'm working with smRNA but found several databases or simply no bases at all for some of them. Can you recommend databases for the next types of smRNA?
Thanks in advance!
Ensembl annotates snoRNAs and snRNAs, so you can use any of their annotations (or even biomart) for those. For piRNAs, I know there's piRNAbank.
Why don't you use RNACentral?
Though I have never used it myself.
I'm playing around with that database now. One thing to note about it is that the dataset you can download via ftp is a mixture of all of the species (not that it's terribly difficult to filter things with biopython). I've yet to find a convenient way to get sequences or coordinates from a single species reliably across source databases (it looks like if you select multiple databases, you only get sequences shared by them).
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version 2.3.6
Any thoughts on this database for snoRNA?
Given that it's human only, seems to be using the hg18 build, and appears to have been last updated a few years ago...
And is there anyway to download the databases (snoRNA and snRNA) instead of loading my datasets? The biomart interface seems a little bit non-intuitive
Either download the GTF for your organism and just filter accordingly or use a biomart query like this, which won't require you to load anything.