A Java-based tool for the design of classification microarrays

Background: Classification microarrays are used for purposes such as identifying strains of bacteria and determining genetic relationships to understand the epidemiology of an infectious disease. For these cases, mixed microarrays, which are composed of DNA from more than one organism, are more effective than conventional microarrays composed of DNA from a single organism. Selection of probes is a key factor in designing successful mixed microarrays because redundant sequences are inefficient and limited representation of diversity can restrict application of the microarray. We have developed a Java-based software tool, called PLASMID, for use in selecting the minimum set of probe sequences needed to classify different groups of plasmids or bacteria. Results: The software program was successfully applied to several different sets of data. The utility of PLASMID was illustrated using existing mixed-plasmid microarray data as well as data from a virtual mixed-genome microarray construct...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Da Meng, Shira L. Broschat, Douglas R. Call
• Keywords: BMCBI 2008, Classification Microarray, Mixed-plasmid Microarrays, Successful Mixed Microarrays