Clote Lab

Computational Molecular Biology

Web engines for teaching tools

• Dot Plot Demo: Dot Plot is a web engine for dot plots of amino acid or nucleotide sequences.

• Path matrix construction: Smith Waterman path matrix and Needleman Wunsch path matrix are web engines to demonstrate the path matrix constructed for optimal local sequence alignment.

• Smith Waterman pairwise alignment: Smith Waterman is a web engine for Smith-Waterman pairwise sequence alignment with linear gap penalty.

• RNA secondary structure prediction: RNAfold is a web interface to local installation of RNAfold from Vienna RNA package of I. Hofacker et al. HTML and Python cgi scripts by P. Clote and J. Santarosa. (Use of Vienna RNA Package in this web interface kindly authorized by Ivo Hofacker.)
  Example using polyadenylation element RNA binding site, experimentally determined by the Hake Lab.

• C5.0 Decision Tree: Interface to local installation of licensed, commercial C5.0 decision tree software from RULEQUEST.
  HTML and Python cgi scripts by P. Clote. Warning: To access this, you must be on the BC local area network.

• DATAMINING with C5.0 and Cubist. Web interface created by M. Elliot, using PHP and extending Python scripts of P. Clote. Warning: To access this, you must be on the BC local area network.