structural alignment

modoc.kesner has asked for the wisdom of the Perl Monks concerning the following question:

Replies are listed 'Best First'.
Re: structural alignment by planetscape (Chancellor) on May 09, 2010 at 23:57 UTC
Perhaps the following would be of interest: Aligning sequence Align::NW Simple String Alignment Search for identical substrings Also, XS Mechanics, which discusses the coding of Align::NW, and has some excellent resources on the Needleman-Wunsch algorithm. Update per biohisham's suggestion: See also BioPerl's implementation of the Smith–Waterman algorithm, at BioPerl's SimpleAlign documentation, or at CPAN's: Bio::SimpleAlign. HTH, planetscape	[reply]
Re: structural alignment by toolic (Bishop) on May 09, 2010 at 23:35 UTC
This may be a good place to start looking: Perl and Bioinformatics	[reply]
Re: structural alignment by biohisham (Priest) on May 10, 2010 at 05:01 UTC
Does anyone know of where I can get code to do protein structural alignments in perl? Welcome to the Monastery first of all. Getting code isn't the goal, since you want to make judgments on whether it fits your requirements according to the type of alignment tasks that you want to perform, that might require you to customize it and maybe break your head over ambiguities in there since you might get to deal with OpenGL and 3-D rendering issues among other things like calculating RMS or figuring torsion angles, structural alignment is a different concept than sequence string alignment and it requires more skills... Since you want to do structural alignments anyways, have you considered the free DeepView since it is an established Structural Alignment Tool and it has a very nice step-wise accompanying tutorial too, so maybe investing time in learning it provides a higher trade-off ... Excellence is an Endeavor of Persistence. Chance Favors a Prepared Mind.	[reply] [d/l]
Re: structural alignment by educated_foo (Vicar) on May 09, 2010 at 22:47 UTC
There are many programs that do protein structural alignment. The amount of work it will take you to choose the one that suits your needs is much greater than the amount of work it will take you to figure out how to use it with Perl. You (or your boss) might be best off hiring someone who knows about structural alignment.	[reply]