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Two tandemly repeated telomere-associated sequences, NP3R and NP4R, have been isolated from Nicotiana plumbaginifolia. Two tandemly repeated telomere-associated sequences in Nicotiana plumbaginifolia.Ĭhen, C M Wang, C T Wang, C J Ho, C H Kao, Y Y Chen, C C DNA sequences may be stored in databases accessible over the internet, obviating the need for the exchange of reference strains. Tandem repeat sequence typing resolves phylogenetic diversity to a level equivalent to PCR ribotypes. Conclusion We conclude that sequence analysis of the two repetitive loci introduced here may be highly useful for routine typing of C.
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Moreover, tandem repeat sequences enabled the reconstruction of the isolates' largely clonal population structure and evolutionary history. difficile isolates comprising 75 ribotypes, tandem repeat sequencing demonstrated excellent concordance with widely used PCR ribotyping and equal discriminatory power. We describe two tandem repeat loci, designated 'TR6' and 'TR10', which display extensive sequence variation that may be useful for sequence-based strain typing. Results This report presents results from a systematic screen for variation in repetitive DNA in the genome of C. Portability of genotyping data is desirable to facilitate inter-laboratory comparisons and epidemiological studies. Typing Clostridium difficile strains based on tandem repeat sequencesīackground Genotyping of epidemic Clostridium difficile strains is necessary to track their emergence and spread. TRAP can also be used to automatically generate annotation data in the format of feature table and GFF files. The results can be generated in convenient formats such as HTML and comma-separated values. TRAP uses the results of the Tandem Repeats Finder program to perform a global analysis of the satellite content of DNA sequences, permitting researchers to easily assess the tandem repeat content for both individual sequences and whole genomes. TRAP, the Tandem Repeats Analysis Program, is a Perl program that provides a unified set of analyses for the selection, classification, quantification and automated annotation of tandemly repeated sequences. Sobreira, Tiago José P Durham, Alan M Gruber, Arthur TRAP: automated classification, quantification and annotation of tandemly repeated sequences.