Ambi, >From Biojava's CE on 2aza.A and 1paz.A, I get: RMSD = 2.8960955657826997 Z-score = 3.7 aligned = 85
and from the original C version: Structure Alignment Calculator, version 1.02, last modified: Jun 15, 2001. CE Algorithm, version 1.00, 1998. Chain 1: pdb/pdb1paz.ent:A (Size=123) Chain 2: pdb/pdb2aza.ent:A (Size=129) Alignment length = 85 Rmsd = 2.90A Z-Score = 3.7 Gaps = 49(57.6%) CPU = 0s Sequence identities = 11.8% The web version of CE is the same except for 1 fewer equivalent residues (CPU/FPU differences?). Can you post your Biojava code? Best, -da On Tue, Jun 7, 2011 at 12:58, Ambikesh Jayal <[email protected]> wrote: > Hi All, > > There seems to be some discrepancy for some protein sequences in results of > Biojava implementation of CE algorithm and the implementation on CE website > http://cl.sdsc.edu/ce/ce_align.html > For example between protein sequences [2aza.A] AND [1paz]. Other such > example are 1cew.I and 1mol.A, 1cid and 2rhe. > > Is there some reason for this discrepancy? > > Results using BioJava implementation of CE algorithm > > ************* [2aza.A] AND [1paz] ************ > CE > afpChain.getTotalRmsdOpt() 2.5267815014062553 > afpChain.getOptLength() 82 > > Results using CE website http://cl.sdsc.edu/ce/ce_align.html > > ************* [2aza.A] AND [1paz] ************ > Rmsd = 2.9Å > Aligned/gap positions = 84/49 > > > > Kind Regards, > Ambi. > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
