I need some information about an salign module
Dear Modellers, The script salign_multiple_struc.py works on sub-optimal alignments as given on page http://computing.bio.cam.ac.uk/local/doc/modeller/node294.html
Tell me, is this script similar to the consistency and sub-optimal alignment generation, as cited by Travis Wheeler for MAFFT, PROBCONS, TCOFFEE. Other than their hydrophobic gap penalties, what is the other difference focusing on alignment strategy between this script and these three servers.
Thank you Ashish
-- Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA
On 8/15/11 9:33 AM, Ashish Runthala wrote: > The script salign_multiple_struc.py works on > sub-optimal alignments as given on page > http://computing.bio.cam.ac.uk/local/doc/modeller/node294.html > > Tell me, is this script similar to the consistency and sub-optimal > alignment generation, as cited by Travis Wheeler for MAFFT, PROBCONS, > TCOFFEE.
Without a reference, the best I can do is tell you how Modeller's suboptimal alignment generation functions, and you can compare the algorithms yourself:
After finding the optimal path through the alignment matrix by dynamic programming, subopt_offset is added to each matrix position on the path and the path reevaluated. Typically this results in a different (sub-optimal) path being found.
Ben Webb, Modeller Caretaker
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Ashish Runthala -
Modeller Caretaker