Difference between revisions of "Applications and libraries/Bioinformatics"

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== The Biohaskell library and applications ==
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== Ketil Malde's Bioinformatics stuff ==
  
   
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;[http://www.ii.uib.no/~ketil/bioinformatics Ketil's bioinformatics pages]
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;[http://malde.org/~ketil/biohaskell/ Ketil's bioinformatics pages]
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:Some tools, implemented in Haskell, are available from this site
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:Some tools and a bioinformatics library, all implemented in Haskell, are available from this site. There is also a [http://blog.malde.org Biohaskell blog], and some [http://www.ii.uib.no/~ketil/bioinformatics/ older web pages].
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* xsact - a sequence clustering tool (currently in revision 1.5).
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* 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.
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* rbr - a sequence masking tool, masking ESTs based on a statistical measure of word frequencies.
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* rselect - a simple and efficient tool for extracting random sets of sequences
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* A bioinformatics library, currently containing bits and pieces needed for the above programs. The main focus at the moment is on nucleotide sequences, but the scope and code base are steadily growing.
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== PolyFARM ==
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;[http://www.aber.ac.uk/en/cs/research/cb/dss/polyfarm/ PolyFARM]
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: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."
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== Other ==
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* [http://www.cs.missouri.edu/~harrisonwl/abstracts.html Bill Harrison]
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* [http://www.techfak.uni-bielefeld.de/ags/pi/ Robert Giegerich's group (AGPI) at Bielefeld University]
   
⚫
* A sequence clustering tool, xsact (currently in revision 1.5).
  
⚫
* A sequence assembly tool, xtract, which uses an interesting algorithm based on de Bruijn graphs, but unfortunately is hard to get to work right. Unless you plan to fix it, use CAP3 instead.
  
⚫
* A sequence masking tool, masking ESTs based on a statistical measure of word frequencies.
  
⚫
* A simple and efficient tool, rselect, for extracting random sets of sequences
  
⚫
* A bioinformatics library, currently containing bits and pieces needed for the above programs.
  
 
{{LibrariesPage}}
  
{{LibrariesPage}}

Revision as of 17:07, 31 December 2010

The Biohaskell library and applications

Ketil's bioinformatics pages
Some tools and a bioinformatics library, all implemented in Haskell, are available from this site. There is also a Biohaskell blog, and some older web pages.
  • 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, but the scope and code base are steadily growing.

PolyFARM

PolyFARM
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."

Other

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

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