New t-gap insertion-deletion-like metrics for DNA hybridization thermodynamic modeling.

We discuss the concept of t-gap block isomorphic subsequences and use it to describe new abstract string metrics that are similar to the Levenshtein insertion-deletion metric. Some of the metrics that we define can be used to model a thermodynamic distance function on single-stranded DNA sequences. Our model captures a key aspect of the nearest neighbor thermodynamic model for hybridized DNA duplexes.

Group testing with DNA chips: generating designs and decoding experiments.

DNA microarrays are a valuable tool for massively parallel DNA-DNA hybridization experiments. Currently, most applications rely on the existence of sequence-specific oligonucleotide probes. In large families of closely related target sequences, such as different virus subtypes, the high degree of similarity often makes it impossible to find a unique probe for every target.

The sequence and analysis of duplication-rich human chromosome 16.

Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin.