We are studying the interaction between lncRNA and miRNA for a particular biological model, and we need to understand the interplay between these. For this we are looking for tools to visualize the interaction or alignment between them. We tried to adapt BLAST to this situation but it was not so interesting.
hi, are you have a pdb file from your complex? do you performed a docking study?
As per my understanding to this question you want to align the
lncRNA and miRNA sequences in a single alignment file ? Am i correct ?
Because alignment will just give you the information about the sequence similarity and not about the interaction between the molecules.
Now coming to your answer, there are several alignment tools like Clustal (W or Omega), Muscle, MAFFT etc. which are available online or on command line interface on local computer.There are many free/commercial software which could be used for the purpose.
I could recommend you to use MAFFT as alignment tool (https://mafft.cbrc.jp/alignment/server/) or Unipro Ugene as a full package free software (http://ugene.net/). But you can choose according to your wish. There are plenty of them, just a google search away.
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