High-density DNA arrays for biological research allow for the detection and expression level measurement of thousands of genes by massively parallel nucleic acid hybridizations. They have tremendous application to medical, agricultural, and environmental research.
DNA arrays for assessing stress and damage caused by pollutants to microorganisms have wide-ranging applications in environmental toxicology, and bioremediation. However, up to 99% of microorganisms in the environment are uncharacterized.
Application of DNA array technology to native organisms in the environment requires detection of families of genes with related but differing sequences. Consensus oligonucleotide probes based on conserved protein sequences have been successfully used to detect related genes. Third-position wobble of the triplicate nucleic acid code for amino acids adds degeneracy to the nucleic acid code, thus requiring degeneracy in hybridization probes.
Until now, design and analysis of consensus-degenerate oligonucleotide probes and PCR primer pairs required the use of multiple programs running on different computer platforms, and extensive manual reformatting of data between applications. This system was not feasible for designing the thousands of probes that can be used on high-density DNA arrays.
A GNU/Linux-based system, called DEgenerate Oligonucleotide Design & Analysis System (DEODAS), for designing and electronically analyzing consensus-degenerate oligonucleotides is being developed by integrating published software tools from other authors: Clustalw, CODEHOP, and EMBOSS. DEODAS integrates these software tools to automatically design and screen oligonucleotides in batch against databases of known gene sequences. This greatly decreases the amount of interactive time required to design and screen probes. Output detailing the designed oligonucleotides is organized in searchable databases that are used to examine and select probes and PCR primers for synthesis and laboratory testing.
Please see the DEODAS manual for full documentation.