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

Question

[f.fassihian]

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

[Michael]

See also:

• Identified Potential Non-Coding Rna, And Then?
• How to use Rfam annotate small RNA and how to see differential expression of novel miRNA produced by mirdeep2?
• How to anntate small-RNA seq reads distribution

Answer 1

[Damian Kao]

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.

Answer 2

[f.fassihian]

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