I have about 20 peptides of variable length (15 amino acids, give or take a few). I ran their predicted structures through Stride to get secondary structure sequences. Example:
amino acid sequence: IEAPSTVPPYPFTQSCYESW
corresponding Stride sequence: CEECHHHHHHTTTCCCEECC
Where each letter in the Stride sequence indicates the type of secondary structure that the corresponding residue is a part of:
H for alpha helix, G for 3-10 helix, I for pi helix, E for Extended beta bridge (a.k.a. beta sheet), B forisolated beta bridge (one pair of aa’s), T for Turn, and C for Coil (none of the above)
I'm looking for a way to do a multiple-alignment of the Stride sequences and get a consensus sequence from them. Any recommendations? I don't need any special scoring matrix; I'll treat each possible substitution equally. Pretty much any bare-bones package for aligning multiple strings should work.
Thanks :)
