I am looking for a program that would be able to perform semi-global (global in query, local in reference sequence) protein alignments fast and efficiently. My query sequences are short (20-30 aa), while reference sequences 10-20 times longer. So far I have been able to find GLSEARCH (from FASTA package) and align, but they seem to be somewhat slow for my task. I would really appreciate it if someone could suggest another alternative.
At least one software that strongly uses the "glocal" terminology is LAGAN, specifically Shuffle-LAGAN
e.g. this website http://genome.lbl.gov/cgi-bin/VistaInput?align_pgm=slagan&num_seqs=2 uses the phrase
Shuffle-LAGAN Glocal pair-wise alignment of finished sequences (detects rearrangements)