A bioinformatics method was used to analyze F/10 and G/11 xylanase basing on principle component analysis, and a model was made to classify between these two folds with an ideal result. The principle components were predicated to be secondary structures, the components were analyzed with the architecture of each family, and found comparable with (beta/alpha)(8)-barrel of F/10 xylanase and right-hand structure of G/11 xylanase. Compared with sequence similarities, this method gave discriminating features a clear meaning. The largest component did not appear in the model, which revealed no difference between these two families. (C) 2004 Elsevier Inc. All rights reserved.