I have +/- 40 RNA sequences that I aligned with ClustalX and fixed (versus the reference secondary structure on this type of RNA) with Bioedit.
My sequences are very big (1500 residues) and they have 6 domains, one of wish - domain 4 - is totally random in sequence - no consensus - and in the number of residues. Yet, the rest produces an aligment I can work with.
I need Bioedit to merge all the residues from the beggining of domain 4 until the end of domain 4 - to then build a covariance model that will focus only in the other domains, the ones that align pretty well.
Is there a way to do this in Bioedit? To merge gaps in a selected region?