I'm doing a project where I need to align three domains (pairwise i.e. 3 different alignments).
The domains have the length of 116, 118 and 124 amino acids, so they are about the same size.
I ran both a local and a global alignment via EMBOSS (default values and used needle for global and water for local).
The local alignment gave the best result (i.e. lowest gap % highest similarity and identity % for all sequences).
However I thought that when you were interested in getting the best alignment of a full sequence that global would be the appropriate choice.
I'm new to bioinformatics so some of my assumptions may be way off. Please help me choose the correct method.