42 Eddy SR: Profile hidden Markov models Bioinformatics 1998, 1

42. Eddy SR: Profile hidden Markov models. Bioinformatics 1998, 14:755–763.PubMedCrossRef

43. Eisenhaber B, Schneider G, Wildpaner M, Eisenhaber F: A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to genome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe . J Mol Biol 2004, 337:243–253.PubMedCrossRef Authors’ contributions All authors read and approved the final version of the paper. NM was the main author of the paper and participated in CAZy annotation and Erastin solubility dmso experimental validation. ED contributed to the experimental work on biofilm formation. PMC participated and supervised the CAZy annotation. SMC contributed to the interpretation selleck inhibitor of the results. BH participated and supervised the CAZy annotation and contributed to the manuscript. ER supervised the experimental work and contributed to the manuscript.”
“Background Helicobacter pylori (H. pylori) is a spiral-shaped, Gram-negative bacterium find more that infects half the world’s population and is the major cause of chronic gastritis, peptic ulcers and gastric malignancies, including gastric non-cardia adenocarcinoma and mucosal-associated lymphoid tissue lymphoma [1, 2]. Most infected individuals

present with no clinical symptoms, but approximately 10~20% will develop peptic ulcers and 1% will develop gastric cancer [3, 4], which could be associated with the diversity of H. pylori. H. pylori exhibits exceptionally high rates of DNA point mutations and intra- and inter-genomic recombination. Recently, many molecular typing tools have been developed to investigate genetic relatedness among H. pylori isolates. However, these methods have limitations including lower discrimination power, or preventing results from different labs being compared [5, 6]. In 1999, MLVA analysis was proposed as a general approach to providing accurate, Epothilone B (EPO906, Patupilone) portable data that were appropriate for the epidemiological investigation of bacterial pathogens

[7–11]. However, there’s little information concerning populations of H. pylori species using MLVA. Whether this method is available for the H. pylori population is still uncertain. H. pylori infections in China are common and extensively distributed, with an average infection rate of about 58%. In this study, 12 VNTR loci of the H. pylori genome were identified and used to analyze 202 strains of H. pylori which originated from different regions of China and Japan. Results Multi-VNTR loci for H. pylori genome PCR products amplified from the reference strains 26695, HPAG1 and J99 were identical to the published sequences sizes. Of the locus VNTR-2576 and VNTR-614, the PCR products sequencing were consistence with our electrophoresis results. The exact number of tandem repeats at each locus could be determined from the sizes of the PCR products. In this study, 30 VNTR loci were candidated from the H. pylori database.

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