[Biojava-l] Biojava implementation of CE algorithm

[Ambikesh Jayal]

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.