I did a structure-based alignment using STRAP and edited this manually using BioEdit. Unfortunately, I forgot to add the full-length sequences of some of these proteins, which would be necessary, since several of them are lacking amino acids in the structure, which are then of course missing in the MSA. It's mainly terminal residues missing, so the core alignment is fine. They shall be aligned by their sequence, but as soon as I put the full-length sequences in BioEdit and run ClustalW or whatever application, it breaks up the entire alignment (which means a lot of work to do the manual refinement again). Is there an option to prohibit this core alignment to be broken up while aligning the full-length sequences?
In case there is not: Which other tools could you recommend to do this procedure?
Surely you can do it outside BioEdit with tools like muscle, mafft, t-coffee, hmmer or maybe even clustal. See discussion in the attached thread.
https://www.biostars.org/p/4901/
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