From: Buz B. <bu...@ma...> - 2009-06-30 21:24:27
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Hi All, I have a very large library (almost 1000) of similar genetic sequences, for which I would like to generate homology models. Does anyone know of a way to automate requests to a homology modeling server, such as SWISS-Model through pymol, or alternatively through python? Thanks! and all the best, --Buz |
From: Donnie B. <dbe...@ge...> - 2009-07-10 04:38:48
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On 17:24 Tue 30 Jun , Buz Barstow wrote: > I have a very large library (almost 1000) of similar genetic > sequences, for which I would like to generate homology models. Does > anyone know of a way to automate requests to a homology modeling > server, such as SWISS-Model through pymol, or alternatively through > python? There's a framework called Biskit that you can use to do it all locally. -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University |
From: Donnie B. <dbe...@ge...> - 2009-07-10 04:55:37
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On 21:38 Thu 09 Jul , Donnie Berkholz wrote: > On 17:24 Tue 30 Jun , Buz Barstow wrote: > > I have a very large library (almost 1000) of similar genetic > > sequences, for which I would like to generate homology models. Does > > anyone know of a way to automate requests to a homology modeling > > server, such as SWISS-Model through pymol, or alternatively through > > python? > > There's a framework called Biskit that you can use to do it all locally. Sorry about the duplication, catching up on my email in order and didn't notice that someone broke the threading. -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University |
From: Nathaniel E. <nat...@gm...> - 2009-06-30 21:49:10
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On Tue, Jun 30, 2009 at 2:24 PM, Buz Barstow <bu...@ma...> wrote: > I have a very large library (almost 1000) of similar genetic > sequences, for which I would like to generate homology models. Does > anyone know of a way to automate requests to a homology modeling > server, such as SWISS-Model through pymol, or alternatively through > python? I believe Modeller uses Python - never tried it myself, though. There is a server for Modeller but academic users can download the program itself. There is in fact an API for using SWISS-Model from a Perl script (which could probably be converted to Python, or wrapped by a Python script), which I used years ago for a similar project. As far as I know this is unpublished, probably because they don't want people to trash their server, but they were happy to supply it when I contacted the site maintainer. They asked that I limit the frequency of my requests, however. I would recommend emailing them. (I have no idea how Modeller compares to SWISS-Model, but I suspect it's more rigorous, especially when sequence homology is remote.) There are other ways to go about this - bioinformaticists have been abusing online databases and servers like this for years - but it's considered bad etiquette to do this without permission (and some groups explicitly forbid this use). -Nat |