Difference between revisions of "Applications and libraries/Bioinformatics"

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Revision as of 18:41, 2 May 2007

Ketil Malde's Bioinformatics stuff

Ketil's bioinformatics pages
Some tools, implemented in Haskell, are available from this site
  • xsact - a sequence clustering tool (currently in revision 1.5).
  • xtract - a sequence assembly tool which uses an interesting algorithm based on de Bruijn graphs, but unfortunately is hard to tune to give optimal results. Unless you plan to fix it, use CAP3 instead.
  • rbr - a sequence masking tool, masking ESTs based on a statistical measure of word frequencies.
  • rselect - a simple and efficient tool for extracting random sets of sequences
  • A bioinformatics library, currently containing bits and pieces needed for the above programs. The main focus at the moment is on nucleotide sequences.


PolyFARM (Poly-machine First-order Association Rule Mining) is a data mining program which finds first order associations in Datalog data. It is based on the ideas from WARMR (L. Dehaspe and L. De Raedt (1997) Mining Association Rules in Multiple Relations. It is described in Clare, A. and King R.D. (2003) "Data mining the yeast genome in a lazy functional language."

This page contains a list of libraries and tools in a certain category. For a comprehensive list of such pages, see Applications and libraries.