[Biojava-l] Biojava implementation of CE algorithm

[Daniel Asarnow]

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 <ambi1999 at gmail.com> 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.
>
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