Hello guys, newbie here.
I have 15 microRNA sequences from rats. I used Velvet and SSPACE to assemble the genomes. Assembeled genomes are 8-9 Mbp, what I am targeting is apply MSA and get consensus within these 15 genomes and then do the genome annotation on that consensus seq. I tried, Clustalx, Kalign, Muscle etc. no result. Lately I have tried Mauve but I could not get any consensus from Mauve. Can anyone help me with this?