I have a protein of interest which is ~300 amino acids in length. I also have around 40 short sequences (all 9 amino acids in length); these are all very different from each other. I would like to perform multiple pairwise alignments to see if these sequences match up with (or have high sequence identity similarity) any areas in the protein of interest.
Since the short 9-a.a. sequences are very heterogeneous, they will have similarities in different regions of the protein of interest. I would like to know if it is possible to perform the alignments for all 40 sequences in one step, rather than using COBALT 40 times (and checking each of the short sequences against the reference sequence individually).
Please let me know if the description of my problem is not clear enough, I would appreciate any help in identifying a way to do this.