Haskell in bioinformatics

Robert Giegerich's group has implemented dynamic programming algorithms in Haskell, including those involved in RNA folding grammars.

• Malde K, Giegerich R. Calculating PSSM probabilities with lazy dynamic programming, Journal of Functional Programming. 2006, 16(1):75-81.
• 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. Print 2004.

Several applications and a Haskell library for bioinformatics is available from http://malde.org/~ketil, with some related publications:

• 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.