Barcodes for genomes and applications

Abstract

Background: Each genome has a stable distribution of the combined frequency for each k-mer and its reverse complement measured in sequence fragments as short as 1000 bps across the whole genome, for 1<k<6. The collection of these k-mer frequency distributions is unique to each genome and termed the genome's barcode.

Computational Challenges in Deciphering Genomic Structures of Bacteria

“…For example, N (4) = 136. Our first observation is that the combined k-mer frequency distribution is highly stable across the whole genome, for any fixed k-mer; and this is true for any sequenced genome, prokaryotic or eukaryotic, chromosomal or organelle [55] .…”

“…Various computational techniques have been developed for characterizing and identifying these mobile elements [19][20][52][53][54] . While the prediction of the MGEs has reached a good level of maturity, reliable prediction of HTGs remains a very challenging problem [55][56][57][58] .…”

“…We have recently developed a simple but yet very effective method for visualizing genomes [55] , through which numerous non-trivial genomic features become visually obvious. The basic idea of this genomevisualization technique is that for a given genome, we partition its sequence into a series of non-overlapping and equal-sized fragments of M bps; then for each k-mer, for any fixed integer k between 1 and 7, we calculate the combined frequency of the k-mer and its reverse complement within each partitioned fragment.…”

Áp Dụng Mô Hình Ẩn Kết Hợp Thuật Toán Bimeta Trong Việc Gom Nhóm Trình Tự Metagenomic

“…Vì vậy, để áp dụng mô hình ẩn cho việc phân tích trình tự metagenomic, cần chuyển đổi trình tự (là một dạng một chuỗi ký tự hợp thành từ 4 ký tự A, G, T, C) thành các từ có độ dài k-mer, ứng với mỗi từ trong tài liệu. Theo [14,18], k=4 được đánh giá là phù hợp.…”

The Self-Organized Chaos Game Representation for Genomic Signatures Analysis

“…Some of the GS are based on information theory concepts [7], others rely on statistical properties [9,8,11,12], and some others state that what is important is the spatial information between sequences [4,13]. All GS proposals depend on the idea that phylogenetically close genomes have similar GS, while phylogenetically distant organisms present different GS.…”