Optimal Probing Patterns for Sequencing by Hybridization

Sequencing by Hybridization by Cooperating Direct and Reverse Spectra

DNA sequencing by hybridization, potentially a powerful alternative to standard wet lab techniques, has received renewed interest after a novel probing scheme has been recently proposed whose performance for the first time asymptotically meets the information theory bound. After settlement of the question of asymptotic performance, there remains the issue of algorithmic fine tunings aimed at im...

Dealing with errors in interactive sequencing by hybridization

MOTIVATION A realistic approach to sequencing by hybridization must deal with realistic sequencing errors. The results of such a method can surely be applied to similar sequencing tasks. RESULTS We provide the first algorithms for interactive sequencing by hybridization which are robust in the presence of hybridization errors. Under a strong error model allowing both positive and negative hyb...

Optimal Sequencing By Hybridization in Rounds

DNA Sequencing by Hybridization Using Semi-Degenerate Bases

One way to enhance the performance of hybridization microarrrays for DNA de novo sequencing is the use of probing patterns with gaps of unsampled positions. Ideally, such gaps could be realized by the inclusion into microarray oligos (probes) of wild-card compounds, referred to as universal bases (which bind nonspecifically to natural bases). The suggested alternative is to deploy in the gap po...

Gene Probe Designing for Evaluation of the Diversity of Bradyrhizobium japonicum Isolates

Many researchers consider the use of different probes for hybridization assays as suitable for studying the genetic diversity of nitrogen fixing bacteria. In this study for asessing genetic diversity among Bradyrhizobium japonicum isolates, two different probes (sucA and topA) chosen from the chromosomal genome of Bradyrhizobium strain USDA 110 were designed, evaluated by DNAMAN software and im...