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?
With Jalview (my preferred multiple alignment viewer/editor) you can select columns (e.g. domain 4), copy them and paste in a new alignment window; then you can "remove all gaps", realign, remove redundancy or whatever you want to do
HTH,
Federico
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abascalfederico
Thank you for your alternate suggestion Federico. I am making a scrip in Python as an alternative solution - for these specific 40 sequences in this specific problem that start at a specific position in BioEdit. But please, other BioStars users, if there is a way to do it in BioEdit, share it with me.
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