Aligning miRNA sequences

Question

[Bioaln]

Hello. I've been recently dealing with miRNA sequences and aligning them has been somewhat problem to me. I've tried all major alignment software and results seem to be quite different for each aligner. Is there any recommended software for miRNA alignments? Muscle seems the most promising when analysing the results, yet I am not quite sure how to compare various alignment outputs. Thanks for any help.

[Devon Ryan]

Are trying to do multiple sequence alignment of the miRNAs (what MUSCLE does) or did you do small-RNAseq and now need to align that data or something else entirely?

[Bioaln]

I am doing multiple sequence alignment, yes.

[Michael]

Here are the EBI MSA web services: https://www.ebi.ac.uk/Tools/msa/

I am not aware of which one is most suitable for miRNA multiple alignment, but you could make a little benchmark dataset and then compare the alignments generated. However, I see the difficulties you are facing to compare and rate the alignments.

[Bioaln]

Thanks for the info. I used 5 of those tools and I will try to compare them in a statistical manner. What do you mean by benchmark dataset? Is it supposed to reveal differences amongst aligners, if so, thanks again for this info.