Server for quick alignment reliability evaluation
Evaluation of Alignment Reliability
The accuracy of sequence-based predictions are sensitive to alignment quality and automatically generated alignments may not be optimal. The per residue alignment scores calculated by SQUARE can give an important insights into the quality of an alignment. Regions defined as reliably aligned by SQUARE are highly likely to be correctly aligned.
Note that template sequence may be corrected if the sequence does not match with the one stored in the FireDB database. FireDB structures are clustered at 97% homology. See the online help for more information about SQUARE.
1. "Predicting reliable regions in protein alignments from sequence profiles" Tress ML, Jones DT, Valencia A.
J. Mol. Biol. 2003;330:705-718.
2. "SQUARE-determining reliable regions in sequence alignments" Tress ML, Graña O, Valencia A.