Small RNA library annotation tool?

[vebaev]

Hi,
is anyone knows a tool for automatic annotation of human small RNAs libraries from NGS? like this:


if not.... I shoud make one maybe

[nicedad]

I guess Blast2go is able to do this

cheers

[vebaev]

Blast2GO is prity slow as making queries to NCBI for each seq, and here we talked about several millions of small seqs?

[eslondon]

Not really, lots of labs have produced their own sets of scripts/tools, based loosely on the following:

-read mapping clustering (to estimate the real size of the small RNA and the real number of distinct RNAs)
-classification by length and levels of expression (as was shown in paper by John Mattick)
-classification by matching to known small RNA structures (e.g. CD boxes, etc)
-matching to known small RNA databases (microRNAs, Y RNAs, etc.), which can be done by downloading all ncRNAs from Ensembl

Hope it helps

Elia