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Re: [modeller_usage] Regarding align2d & CS-BLAST alignments PLEASE ANSWER ME QUICKER ..I AM STUCK UP IN A FEW CASES

On 09/12/2011 06:27 AM, Ashish Runthala wrote:

I am finding a critical difference in the pairwise alignment
computed by MODELLER and the corresponding alignment cognitive to the
CS-BLAST undertaken alignment.


That doesn't seem surprising. BLAST alignments are local and
approximate; Modeller does rigorous dynamic programming with global or
local alignments using a range of methods for constructing the residue
distance matrix.


Where CS-BLAST has got the altered sequences from, when i precisely
called the PDB for it.


You'll have to ask the CS-BLAST people about that.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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