Difference between revisions of "Applications and libraries/Bioinformatics"

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(The Biohaskell library and applications: Updated outline of BioHaskell libraries.)
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== The Biohaskell library and applications ==
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== The [http://www.biohaskell.org/ Biohaskell library] and applications ==
   
;[http://malde.org/~ketil/biohaskell/ Ketil's bioinformatics pages]
 
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There are [http://biohaskell.org/Libraries three main kinds of the libraries] within BioHaskell project:
: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].
 
   
* xsact - a sequence clustering tool (currently in revision 1.5).
 
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* sequence and alignment processing -- see [http://malde.org/~ketil/biohaskell/ Ketil's bioinformatics] [http://www.ii.uib.no/~ketil/bioinformatics/ pages], and [http://blog.malde.org his blog]. In particular:
* 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.
 
 
** xsact - a sequence clustering tool (currently in revision 1.5).
* rbr - a sequence masking tool, masking ESTs based on a statistical measure of word frequencies.
 
 
** 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.
* rselect - a simple and efficient tool for extracting random sets of sequences
 
 
** 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
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** [http://hackage.haskell.org/package/blastxml blastxml] - parser for Blast XML data output.
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** [http://hackage.haskell.org/package/blastHTTP blastHTTP] - tool to query [http://blast.ncbi.nlm.nih.gov/ NCBI Blast service]
   
* 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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* RNA secondary structure tools, some of them using [http://www.tbi.univie.ac.at/~choener/adpfusion/ ADPFusion framework] from [http://www.techfak.uni-bielefeld.de/ags/pi/pages/bioinformatics.htm Robert Giegerich group].
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* Structural libraries:
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** [http://hackage.haskell.org/package/hPDB hPDB] - fastest parallel Protein Databank parser according to [http://www.biomedcentral.com/1756-0500/6/483/abstract this benchmark].
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** [http://hackage.haskell.org/package/parsestar parseSTAR] - parser for [http://www.bmrb.wisc.edu Biological Magnetic Resonance Bank] data.
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** [http://hackage.haskell.org/package/hTalos hTalos] - parser for [http://spin.niddk.nih.gov/NMRPipe/talos/ TALOS+] output.
   
 
== PolyFARM ==
 
== PolyFARM ==

Revision as of 18:22, 6 December 2013

The Biohaskell library and applications

There are three main kinds of the libraries within BioHaskell project:

  • sequence and alignment processing -- see Ketil's bioinformatics pages, and his blog. In particular:
    • 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
    • blastxml - parser for Blast XML data output.
    • blastHTTP - tool to query NCBI Blast service

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.