Applications and libraries/Bioinformatics

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

• RNA secondary structure tools, some of them using ADPFusion framework from Robert Giegerich group.

• Structural libraries:
  • hPDB - fastest parallel Protein Databank parser according to this benchmark.
  • parseSTAR - parser for Biological Magnetic Resonance Bank data.
  • hTalos - parser for TALOS+ output.

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

• Bill Harrison
• Robert Giegerich's group (AGPI) at Bielefeld University

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