Comparison of metatranscriptomic samples based on k-tuple frequencies.

ABSTRACT:

Background

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 m

SUBMITTER: Wang Y 

PROVIDER: S-EPMC3879298 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature