About the Microarray Manual Curation Tool (MMCT)

This web tool provides a visual mean of estimating the hybridization strength between a probe and a target and the locations on the target where the probe strongly hybridizes with the target. The tool uses a thermodynamic model for DNA/DNA and RNA/RNA hybridization implemented in the MultiRNAFold 1.9 package available at http://www.rnasoft.ca.

The tool accepts as input a microarray chip platform, a probe sequence, a target sequence and the size of a window that will be used to extract sub-target sequences starting from the begining of the target. The sub-target sequences will be hybridized with the probe and each free energy value will be diplayed on a graph. The smaller the free energy value is, the stronger the hybridization is between the probe and the sub-target sequence.

Here is a sample Microarray Manual Curation Tool (MMCT) snapshot image for Affymetrix chip HG_U133A, probe id 1316_at at position 2017 and target id 1316_at.