UNLABELLED The Next Generation Sequencing (NGS) is a state-of-the-art technology that produces high throughput data with high resolution mutation information in the genome. Numerous methods with different efficiencies have been developed to predict mutational effects in the genome. The challenge is to present the results in a balanced manner for better biological insights and interpretation. He...

BACKGROUND The strong geographic structure shown by the global pattern of HBV lineages suggests an ancient origin for this virus; however, estimates based on the molecular clock suggest a very recent origin for the Native American genotypes F and H. In this study, we contribute to this debate by estimating the divergence times of genotypes F and H and by discussing how evolutionary rates estima...

mutations in the human hepatitis b virus (hbv) genome contribute to its escape from host immune surveillance and result in persistent infections. the aim of this study was to characterize the molecular variations of the surface gene and protein in chronically-infected patients from the southern part of iran. the  surface  genes  from  12  hbv  chronic  carriers  were  amplified, sequenced  and ...

It has been suggested that mutation bias is the major determinant of base composition bias at synonymous, intron, and flanking DNA sites in mammals. Here I test this hypothesis using population genetic data from the major histocompatibility genes of several mammalian species. The results of two tests are inconsistent with the mutation hypothesis in coding, noncoding, CpG-island, and non-CpG-isl...

Abstract. We compare conformance checking based on symbolic execution to conformance checking via bounded model checking. The application context is fault-based test case generation, focusing on realtime faults. The existing bounded model checking approach is performed on timed automata. It supports time-relevant mutation operators and a preprocessing functionality for removing silent transitio...

Our understanding of basic evolutionary processes in bacteria is still very limited. For example, multiple recent dating estimates are based on a universal inter-species molecular clock rate, but that rate was calibrated using estimates of geological dates that are no longer accepted. We therefore estimated the short-term rates of mutation and recombination in Helicobacter pylori by sequencing ...

Experimental evolution of short-lived organisms offers the opportunity to study the dynamics of polymorphism over time in a controlled environment. Here, we characterize DNA polymorphism data over time for four genes in bacteriophage T7. Our experiment ran for 2500 generations and populations were sampled after 500, 2000, and 2500 generations. We detect positive selection, purifying ("negative"...

Single-stranded DNA is more subject to mutation than double stranded. During transcription, DNA is transiently single stranded and therefore subject to higher mutagenesis. However, if local intra-strand secondary structures are formed, some bases will be paired and therefore less sensitive to mutation than unpaired bases. Using complete genome sequences of Escherichia coli, we show that local i...

Patterns of codon bias in Drosophila suggest that silent mutations can be classified into two types: unpreferred (slightly deleterious) and preferred (slightly beneficial). Results of previous analyses of polymorphism and divergence in Drosophila simulans were interpreted as supporting a mutation-selection-drift model in which slightly deleterious, silent mutants make significantly greater cont...

Five hundred colonies of lactic acid bacteria (LAB) isolated from Kem-Buk-Nud, a traditional Thai fermented food, were screened for the presence of nisin gene by using the polymerase chain reaction (PCR) with primers specific to nisin A structural gene. A LAB isolate, RP359, identified as Lactococus lactis subsp. lactis was found to give an expected 231-bp PCR product and to have antimicrobial ...