Question: Bioedit: remove all gaps in selected region
0
gravatar for catarina.fa
19 months ago by
Poland
catarina.fa0 wrote:

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?

ADD COMMENTlink modified 19 months ago • written 19 months ago by catarina.fa0
0
gravatar for abascalfederico
19 months ago by
Spain
abascalfederico960 wrote:

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

 

ADD COMMENTlink written 19 months ago by abascalfederico960

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.

ADD REPLYlink written 19 months ago by catarina.fa0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1162 users visited in the last hour