On 7/25/11 10:10 PM, Brian Tsui wrote: > In the output for salign, there is a raw quality score, a percentage > quality score, and many other values. What value should I focus on to > make sure that I have a good alignment? Is there a cutoff that I should > use? If so, are there references that I could cite?
For a structural alignment, there is an objective measure of the "best" alignment - that which maximizes the percentage of residues within the cutoff distance. This is the "quality score", which is roughly similar to the GDT_TS score; see Protein Eng Des Sel 22, 569-574, 2009. Modeller includes an "iterative structural alignment" method which maximizes this score.
For a sequence alignment, you have a tougher job - it depends what you want to use the alignment for. For comparative modeling, one approach is to score the quality of models built using that alignment. See Nucleic Acids Res 31, 3982-3992, 2003.
Ben Webb, Modeller Caretaker