my protein of interest has a length of aka 300 residues. I do a global multiple sequence alignment with a set of homologs and I obtain a phylogenetic tree from there. So far so good.
Now, for a subsequent task, I need to have an accurate MSA of a region of interest of about 50 aminoacids, and I do not care much about the rest. So, what would you guys do in this case? Do I build (or fetch from Pfam) an HMM profile of this region and align with hmmalign? Do I perform a local alignment? How, and with what input?
Thanks a lot!