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Applications and libraries/Bioinformatics

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1 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

2 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."

3 Other

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