I have a list of 15 genes known to be expressed in the yeast plasma membrane. I'd like to try and identify a common localization tag within these sequences. I think I need to perform a local alignment of the sequences rather than a global alignment. I'm using MUSCLE to do the alignment but I'm a bit overwhelmed by all of the options. I've tried a gap penalty of -1, -10 and -100. -10 seems to provide only 2 residues that align, the -1 shows a global alignment and -100 nothing at all.
Any help appreciated on the best settings to use. Should I keep trying different gap settings or should I change a different parameter, or use a different program?
Many thanks. John