Comparison of metatranscriptomic samples based on k-tuple frequencies

PloS One
Ying WangFengzhu Sun

Abstract

The comparison of samples, or beta diversity, is one of the essential problems in ecological studies. Next generation sequencing (NGS) technologies make it possible to obtain large amounts of metagenomic and metatranscriptomic short read sequences across many microbial communities. De novo assembly of the short reads can be especially challenging because the number of genomes and their sequences are generally unknown and the coverage of each genome can be very low, where the traditional alignment-based sequence comparison methods cannot be used. Alignment-free approaches based on k-tuple frequencies, on the other hand, have yielded promising results for the comparison of metagenomic samples. However, it is not known if these approaches can be used for the comparison of metatranscriptome datasets and which dissimilarity measures perform the best. We applied several beta diversity measures based on k-tuple frequencies to real metatranscriptomic datasets from pyrosequencing 454 and Illumina sequencing platforms to evaluate their effectiveness for the clustering of metatranscriptomic samples, including three d2-type dissimilarity measures, one dissimilarity measure in CVTree, one relative entropy based measure S2 and three classica...Continue Reading

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Citations

Feb 2, 2016·Journal of Theoretical Biology·Lianping YangChenhui Yang
Jan 2, 2016·Biochemical and Biophysical Research Communications·Ying WangTing Chen
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Feb 16, 2021·Frontiers in Genetics·Yujie HouYing Wang

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