Difference between revisions of "Applications and libraries/Bioinformatics"

Revision as of 17:07, 31 December 2010

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 (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.

@@ Line 1: / Line 1: @@
 == The Biohaskell library and applications ==
-;[http://malde.org/~ketil/biohaskell Ketil's bioinformatics pages]
+;[http://malde.org/~ketil/biohaskell/ Ketil's bioinformatics pages]
-: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].
+: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).
@@ Line 13: / Line 13: @@
 == PolyFARM ==
-;[http://www.aber.ac.uk/compsci/Research/bio/dss/polyfarm/ PolyFARM]
+;[http://www.aber.ac.uk/en/cs/research/cb/dss/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."