Csharp For Programming In Bioinformatics

Question

[Reyhaneh]

Hi;

I am programming using c#. and I wanted to know if any one knows a c#-based parser for PDB files? the only available c# class libraries I have found are at this site: http://www.kofler.or.at/bioinformatics/biosharp.html. Are there any other sources?

Cheers;

[Michael Schubert]

I don't know what the library is capable of but I think that's one of your best shots: What Do You Think Microsoft Biology Foundation?

[Reyhaneh]

Great! Thank you

Answer 1

[Hamish]

.NET Bio, the successor to Microsoft Biology Foundation (MBF) (mentioned by Michael in the comments), would be worth looking at, but from what I can see it is currently sequence centric and doesn't appear to have support for structure data.

Since Microsoft uses the acronym PDB for a development artefact, Google isn't much help with the obvious search terms... however rummaging around on CodePlex does find a couple of structure visualisation tools, which may be worth looking into:

• Protein Insight
• 3D Molecule Viewer

Another option which may be worth considering is using the multi-language support in .NET to use a PDB parser implementation from another language. This provides the option of using one of the more mature bioinformatics libraries from your C# code. So you could use:

• BioJava via IKVM.NET
• BioPython via IronPython
• BioRuby via IronRuby

While this is a little more complex to set-up than a C# implementation, it will provide access to most of the features available in these libraries.

[Reyhaneh]

Thanks for the useful information.