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.
SQUARE can be used to improve alignments. SQUARE also provides optimal alignments, secondary structure information and functional important that can be used to help adjust alignments.
The server will generate 3D structures based on the template that are coloured by alignment reliability. By sending the alignment you will automatically generate the model CA trace.
The alignment must contain one sequence that has good similarity to a known structure (the template). All fields are required. At present we can only accept alignments in fasta format with the template sequence in the second position. The template PDB code and the chain identifier are compulsory.
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.
 Predicting reliable regions in protein alignments from sequence profiles. Tress ML, Jones D, Valencia A.
Journal of Molecular Biology. Volume 330, Issue 4, 18 July 2003, Pages 705-718;
 SQUARE--determining reliable regions in sequence alignments. Tress ML, Graña O, Valencia A.
Bioinformatics, Volume 20, Issue 6, 12 April 2004, Pages 974-975;
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