Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information

Background: Expression microarrays are increasingly used to characterize environmental responses and hostparasite interactions for many different organisms. Probe selection for cDNA microarrays using expressed sequence tags (ESTs) is challenging due to high sequence redundancy and potential cross-hybridization between paralogous genes. In organisms with limited genomic information, like marine organisms, this challenge is even greater due to annotation uncertainty. No general tool is available for cDNA microarray probe selection for these organisms. Therefore, the goal of the design procedure described here is to select a subset of ESTs that will minimize sequence redundancy and characterize potential cross-hybridization while providing functionally representative probes. Results: Sequence similarity between ESTs, quantified by the E-value of pair-wise alignment, was used as a surrogate for expected hybridization between corresponding sequences. Using this value as a measure of dissim...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Yian A. Chen, David J. Mckillen, Shuyuan Wu, Matthew J. Jenny, Robert Chapman, Paul S. Gross, Gregory W. Warr, Jonas S. Almeida
• Keywords: BMCBI 2004, Microarray Probe, Sequence Diversity, Sequence Redundancy