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Estimating the distribution of small non-coding RNAs among the reads: Which annotation database / r-Package?

Hi everybody,

I am working on miRNAs derived from plasma exosomes. I have already mapped my small RNA sequences against human genome and mature miRNAs from mirBase to get the known miRNAs. Now, I would like to annotate the reads that could not be identified as miRNAs to find the distribution of other RNA species in the exosomes. Could somebody suggest me an R package for annotation or an annotation database for other RNA species? (I have already used blastn to detect other small non-coding RNAs. But this does not help me to get what I mentioned above.)

Many thanks in advance

mirna annotation small non-coding rna r-package
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written by f.fassihian • f.fassihian

2 answers

RFAM (http://rfam.xfam.org/) has a collection of various RNA classifications. You'll probably have to navigate their ftp data files to find specifically what you are looking for though.

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written by Damian Kao Damian Kao

Thanks a lot for your tips! I'm going to use RFAM.

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written by f.fassihian • f.fassihian

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