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We describe principal component method for the DNA sequence analysis using digital filters. With the huge amount of data accessible in the public domain, digital filters are very helpful in DNA sequence processing. In this technique, the occurrence frequency of the q-gram genetic word of interest is determined from the DNA sequence. The sequence is then elucidated by using finite impulse response...
In this study, we analyzed the diversity of vaginal microbiota in 9 bacterial vaginosis (BV) positive and 11 healthy women from the metropolitan area of Guangzhou in Southern China using full-length 16S rDNA. Our data confirmed that a shift in the abundance of bacterial species present in the vaginal environment comparing the BV and non-BV groups. Each sequence read was assigned to a genus or a species...
Fourier-transform infrared spectroscopy (FT-IR) utilizes nanostructural differences between bacterial cells for the rapid identification, classification, and differentiation of many species of bacteria, but most studies have used only live cells. A rapid and reliable method for determining the total number of live and dead bacterial cells in a food could prevent the distribution of unsafe products...
In this paper we have investigated linear combinations of oligonucleotide (k-mer) frequencies for binning the metagenomic DNA fragments of short-to-moderate lengths. The k-mer frequencies have been widely used for gene prediction, phylogenetic tree construction, and metagenomic binning. However, the k-mer frequencies will lead to a high dimensional feature space even for a modest value of k. Existing...
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