MOTIVATION The methods for analyzing overlap data are distinct from those for analyzing probe data, making integration of the two forms awkward. Conversion of overlap data to probe-like data elements would facilitate comparison and uniform integration of overlap data and probe data using software developed for analysis of STS data. RESULTS We show that overlap data can be effectively converte...

Bayesian inference often requires approximating the posterior distribution with Markov Chain Monte Carlo (MCMC) sampling. A central problem with MCMC is how to detect whether the simulation has converged. The samples come from the true posterior distribution only after convergence. A common solution is to start several simulations from different starting points, and measure overlap of the diffe...

Human papilloma virus (HPV) is the major cause of invasive cervical cancer (ICC). The study aim was to determine the prevalence of HPV genotypes and to correlate HPV types with response to radiotherapy. A total of 43 cervical biopsies collected from sequentially enrolled patients were analyzed by DNA amplification with MY09/MY11 primers and sequenced to determine the HPV genotype. Samples with ...

This paper introduces a new way of representing bankruptcy rules. These representations are used to show that the minimal overlap rule is a composition of the Ibn Ezra rule and the constrained equal losses rule, a result originally obtained by [1]. The residual minimal overlap rule is analysed as an alternative extension of the Ibn Ezra rule, by using a composition with the constrained equal aw...

This chapter introduces the FastPCR software as an integrated tool environment for PCR primer and probe design, which predicts properties of oligonucleotides based on experimental studies of the PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations. These include the standard PCR as well as the multiplex, long-dista...

Finishing is rate limiting for genome projects, and improvements in the efficiency of complete genome-sequence compilation will require improved protocols for gap closure. Here we report a novel approach for extending shotgun contigs and closing gaps that we termed PCR-assisted contig extension (PACE). PACE depends on the capture of rare mismatched interactions that occur between arbitrary prim...