Haskell for Bioinformatics
2009 June 16
Ketil Malde has developed a functional-flavored bioinformatics library in Haskell for building bioinformatics related tools and utilities. As of now library includes a collection of data structures and algorithms, and most of the features are stable, robust, and well-documented. A detailed description is available from download website. Malde also maintains a blog featuring tutorials and articles using Bio-Haskell. We are also well aware about power of Haskell for information visualization and visual analytics and now when we have libraries to manipulate biological data it seems reasonable to create more robust bioinformatics visualization in Haskell. For example, ProteinVis-a tree viewer for hierarchical clustering of proteins in the human Genome. At first ProteinVis gives an impression of Circos, a tool commonly used to create aesthetic visualizations for comparative genomics data, but on close inspection one can find powerful visual anlytics feature of ProteinVis which provides interactive way to explore proteins and their shared gene ontology structure.
ProteinVis Apart from above you can also read few interesting papers describing implementation of Haskell in Bioinformatics
- Steffen P, Giegerich R. Versatile and declarative dynamic programming using pair algebras. BMC Bioinformatics. 2005 Sep 12;6:224.
- Giegerich R. A systematic approach to dynamic programming in bioinformatics. Bioinformatics. 2000 Aug;16(8):665-77.
- Giegerich R, Voss B, Rehmsmeier M. Abstract shapes of RNA. Nucleic Acids Res. 2004 Sep 15;32(16):4843-51.
- Malde K, Coward E, Jonassen I. Fast sequence clustering using a suffix array algorithm. Bioinformatics. 2003 Jul 1;19(10):1221-6.
- Malde K, Schneeberger K, Coward E, Jonassen I. RBR: library-less repeat detection for ESTs. Bioinformatics. 2006 Sep 15;22(18):2232-6. Epub 2006 Jul 12.
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Haskell for Bioinformatics: Ketil Malde has developed a functional-flavored bioinformatics library in Haskell fo.. http://tinyurl.com/mr4nyt
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