Figure 2From: Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray developmentStrategy to design explorative probes for functional microarrays used in Metabolic Design. After extraction of potential candidate sequences by BLASTp using query reference protein to compare against concatenated Swiss-Prot and TrEMBL databases, a multiple alignment with selected protein sequences and the reference protein is performed. The next step is in two parts: (i) for each molecular site, amino acids are backtranslated, taking into account all genetic code redundancy to determine a degenerate nucleic consensus sequence, (ii) probes are then extracted from this consensus sequence, according to defined user parameters. The program then searches for all potential cross-hybridizations for each selected probe against the 'Cross-hybridization database' by tBLASTn. Kane's criteria are then checked for all positive results by BLASTn. If Kane's criteria are in agreement with a potential cross-hybridization, the program also checks whether it is a potential member of the targeted enzyme family using a BLASTx comparison against the reference protein. Cross-hybridization results are then clustered by BLASTn, stored and visualized in an output file.Back to article page