Common elements within two set of miRNAs

[Giorgio C]

Hi all,

i have two set of miRNAs from a 454 run. Now my question is how i can clusterize common elements from the two set ? For "common" i mean sequences that differ at most by 2 nucleotides ! Is there any tool that can do this automatically ?

Thank you

[jjohnson]

Hi Georgio,

I would check out CLCBio (or maybe another vendor - but we have used CLCBio for this). They have a great miRNA analysis pipeline. First you need to detect and trim the adapter, then cluster, and you can also annotate against know miRNAs (such as mIRBase, ncRNA.org, etc) using the software. Its free to try for 30 days, and if you like it, it usually pays for itself in short order, especially if you are doing other NGS stuff.

Let me know how it goes.