Difference between revisions of "Applications and libraries/Bioinformatics"

Revision as of 09:39, 6 December 2006

Ketil's bioinformatics pages: Some tools, implemented in Haskell, are available from this site

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.

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 4: / Line 4: @@
 :Some tools, implemented in Haskell, are available from this site
-* A sequence clustering tool, xsact (currently in revision 1.5).
+* xsact - a sequence clustering tool (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.
+* 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.
-* A sequence masking tool, masking ESTs based on a statistical measure of word frequencies.
+* rbr - 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
+* 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.
+* A bioinformatics library, currently containing bits and pieces needed for the above programs.  The main focus at the moment is on nucleotide sequences.
 {{LibrariesPage}}