Program in Mathematics and Molecular Biology

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SIMON CAWLEY

Model-Based Basecalling

Using standard HMMís leads to good results in the basecalling of DNA sequences. An HMM has been developed and compared with some of the other technologies available for doing the same task. While not as good as the best, it has been shown to perform well. Since the signal to be basecalled is inherently nonstationary, an inhomogeneous HMM should fit the data better and will hopefully lead to improved basecalling. Such a model has been designed and is currently in development.

Transposon-Mediated Sequencing

A new method for evaluating coverage probabilities for transposon mediated sequencing has been developed and empirically evaluated. This was used to design a method for optimally selecting transposons to achieving double stranded coverage for DNA sequences of 2-Skb in length. The method has been implemented and is now in daily use at the Berkeley Drosophila Genome Project.

 
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