Bioedit: remove all gaps in selected region

Question

[catarina.fa]

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?

Answer 1

[abascalfederico]

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

[catarina.fa]

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.