small non-coding RNA
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6.6 years ago
biofalconch ▴ 470

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? :

piRNA

snoRNA

snRNA

 

Thanks in advance!

smRNA databases • 1.4k views
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6.6 years ago

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.

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Any thoughts on this database for snoRNA? https://www-snorna.biotoul.fr/getseq.php

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Given that it's human only, seems to be using the hg18 build, and appears to have been last updated a few years ago...

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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

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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.

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6.6 years ago
Chirag Nepal ★ 2.3k

Why don't you use RNACentral ?

http://rnacentral.org/

Though i have never used it myself.

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That looks like a nice one stop shop. I'd never heard of it before, thanks for pointing it out.

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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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