Bram Veldhoen

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Hirschberg Global Alignment in C# .NET 2.0

This post is about some work I did in 2006 regarding the Hirschberg Global Alignment algorithm. The main reason I'm blogging about this is because, even though I do not work in the field of bioinformatics, and I am far from being a proper bioinformatician, I'm curious to know if C# (and .NET or mono) is used by others in the field of bioinformatics. So, if you read this, drop me a line!

What is the Hirschberg Global Alignment algorithm?

Some descriptions can be found at the following sites:

What can the algorithm do?

The algorithm allows for finding the best alignment of sequences, such as DNA or protein sequences. More importantly, it can do it in n space, rather than in n2 space, which obviously is important for long sequences. Some examples, that the implementation, referred to below, produces:

ATG-
-TGA
 
ACGCTG-A
-CGCTGAA
 
TTTTG----GGG 
TTTTAAAAGGGG 
    
GTCGGGA-GACC-TTA----GGACGT
AT--G-ATGACCCTTAAAAAG--C-C
 

Why did I do it?

In September 2006, I started an academic course on "Algorithms for Genomes" (A4G) at the IBIVU Amsterdam (http://www.ibi.vu.nl/teaching/a4g/). Part of this excellent course consisted of implementing the Hirschberg Global Alignment algorithm. As I had experience with C#, I chose to implement it in C# .NET. Afterwards, I got laughed at by my unix oriented bioinformatics teacher for choosing C#. I never got over it. :)

In order to get my implementation evaluated for grading, I had to make sure it ran on the mono framework. I used the 1.1.12 version at the time, but I haven't checked since if the code is still compatible with the latest version of the mono framework.

Where can you find the code?

http://www.codeplex.com/HirschbergCSharp.

Print | posted on Saturday, January 26, 2008 3:15 PM |

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# re: Hirschberg Global Alignment in C# .NET 2.0

I should probably do another posting, but I have posted once on my use of C# in an industrial bioinformatics setting (which also yielded one strong negative response!). There are a few bits of code floating about, which I'll try to tally up sometime

http://omicsomics.blogspot.com/2007/10/opus-173-programming-on-dark-side-c.html
7/25/2008 4:22 AM | Keith Robison
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# re: Hirschberg Global Alignment in C# .NET 2.0

Hehe, thats cool I'm on IBIVU now and people are still looking unfavorably on me for using c# :) Thanks for the hirschberg anyway
2/28/2009 3:22 AM | jan
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