Thank you Jason.


On Wed, Apr 17, 2013 at 10:18 AM, Jason Vertrees <> wrote:
Hi Quyen,

It's been a few years since I wrote that but here is what I recall:

D0 is a constant cutoff that represents the upper bound of dissimilarity for the difference of two distance matrices A_i and B_j, rooted at subsequences i to i+8 and j to j+8, respectively. Raising this value allows for sloppier fragments being considered.

D1 is a constant cutoff that represents the upper bound of dissimilarity for the entire path being considered. In fact, it's equal to path_score / (window_size * path_length).

So, D0 ensure that incoming fragments are still good. D1 ensures that as we extend the current alignment the total quality of the current alignment remains good.

After this, all N top scoring paths are stored in the path cache and the best path is returned.


-- Jason

On Wed, Apr 17, 2013 at 3:34 AM, QT <> wrote:
Dear all,

I have a question regarding CEalign d0 and d1 parameter.  What exactly are their functions?

I don't know enough C++ to decipher the algorithm but they are used findPath() in ccealignmodule.cpp.  It seems that that d0 controls a similarity matrix and d1 the path length.  A d1 below a certain number does indeed make cealign return RMSD over smaller set of residues and there is a lower bound for d1 where cealign will fail to align.  D0 behaves similarly.  The default is 2 and 3 for d0 and d1.  I'm going to guess that those numbers are also dimensionless.

Will it be useful to tune the parameter d0 and d1?


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Jason Vertrees, PhD
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