snRNA annotation in genome

Question

[E]

Hi,

I would like to annotate all small RNAs in a genome based on different databases (e.g. miRBase) with the purpose of generating a gff file I can use for further analysis (and to practice).

I searched for tools to achieve this and my ideal tool has the following qualities: 1. I can provide various databases at the same time which are searched subsequently 2. A genome file not RNA-seq data is annotated.

Unfortunately all the tools I have found so far are not capable of doing so.
(This is what I found and why I don't ant to use it: Infernal is rather focused on structure based search and you can only use one DB for search, Unitas uses RNA-seq data as input, I do not get what database ShortStack is using)

Does anybody have recommendations which tool I can use? Also, if there are different possibilities of using databases for annotation I am happy for every hint ;)

This is rather new to me therefore, sorry if I missed a post already covering this or got something general wrong.

Cheers

Answer 1

[Puli Chandramouli Reddy]

Both snoscan and miR-PREFeR can be used and are compatible with MAKER pipeline. For further reading about it.

[E]

Hi Puli, thank you for the answer but I am not sure if I can use these tools. As far as I understand it, snoscans looks for 2'-O methylation sno guide RNAs and miR-PREFeR predicts miRNAs in plants.

I am looking for a tool that allows me to annotate small RNAs (siRNAs, piRNAs, miRNAs) in a genome with the help of pr- existing databases . Do you maybe also know a tool that does this?

Thanks again

[Puli Chandramouli Reddy]

Sorry I assumed your are working on plants. to my knowledge there is no single effective tools to predict si/miRNA in animals due to differences in complementarity (except in some basal eumetazoans ).

I found an interseting pipeline mentioned in this book chapter. Here, they used

1. structure based tools such as Einverted and RNAfold (which you have tried, I guess)
2. Filter these outputs using MiRcheck.
3. use BLAST to find out known miRNAs
4. finally use these to train miRNA-SOM to predict other/novel miRNA.

I think even BLASTN using extracted hairpin sequences from different databases (miRBase etc.) followed by filters for loop (gap size of inverted repeats) can be done (this is purely my suggestion and have not tried).