Gotoh Implementation of Smithwaterman in Perl or Bioperl

Question

[swttalyan]

Hi,

I am looking for the Gotoh Implementationm of Smithwaterman(optimized) in perl or Bioperl which is has computational complexity O ( mn ) .It will be good if someone who have already implemented this can share with me and also if it possible to use custom substitution matrix in the implementation.

Thanking you in advance for the help.

Best Sweta

Answer 1

[Jean-Karim Heriche]

Bioperl has Bio::Tools::dpAlign. It doesn't use Gotoh's optimization though but the Miller-Myers' implementation because it is superior (see details here).