Abstract
The ability to calculate the correct sequence alignment is crucial to many types of studies. The accuracy in alignment is critical in predicting gene ancestry, the number and location of point mutations, evolutionary distance and phylogeny. A study was conducted to test the biological significance of PIR pairwise alignment using 40 N-terminal signal peptides of different taxonomic origin and having various functions. Our results suggest that PIR pairwise alignment is not ideal for some proteins with N-terminal signal peptides, because it produces an erroneous alignment that lacks both statistical and biological significances. This communication discusses the shortcomings in the PIR pairwise alignment tool and calls for a cautious approach while using it for signal peptides.