Clustering of miRNAs from a variety of species

Question

[biolab]

Dear all

I am trying to align many miRNAs from a variety species, and then auotomatically get miRNA clustering information. MUSCLE or CLUSALW can do alignment (I guess these two tools can align short sequences), but how to get clustering information (e.g., group1 contains miR-1 of species 1 and miR-10 of species2; group2 contains miR-20 of species 1 and miR-13 of species 3)?

I should note only relying on nomenclature at miRBase for miR grouping is not accurate, so sequence alignment is needed.

Any of your comments or answers will be helpful for me. THANKS!

[Juke34]

I guess, a good start would be to perform a clustering using a tool such as DNAClust or by playing with Cap3 (as described here... It is not dedicated to do that, but you can use this approach if you lower the similarity threshold.)

Once the clusters created, you have to write a simple script that reads them one by one and displays the information that interest you.

[biolab]

Thanks a lot, Juke-34, your answer is much helpful!