Structural visualization of sequential DNA data

Autor:	Jing-hua Fu, Qun-sheng Peng, Shiaofen Fang, Qian You, Wei Chen, Xiao-hong Mao
Rok vydání:	2011
Předmět:	Whole genome sequencing ComputingMethodologies_PATTERNRECOGNITION Property (programming) Computer science Feature vector General Engineering Visual Word Computational biology Genome Algorithm Genome size DNA sequencing Visualization
Zdroj:	Journal of Zhejiang University SCIENCE C. 12:263-272
ISSN:	1869-196X 1869-1951
DOI:	10.1631/jzus.c1000091
Popis:	To date, comparing and visualizing genome sequences remain challenging due to the large genome size. Existing approaches take advantage of the stable property of oligonucleotides and exhibit the main characteristics of the whole genome, yet they commonly fail to show progression patterns of the genome adjustably. This paper presents a novel visual encoding technique, which not only supports the binning process (phylogenetic analysis), but also allows the sequential analysis of the genome. The key idea is to regard the combination of each k-nucleotide and its reverse complement as a visual word, and to represent a long genome sequence with a list of local statistical feature vectors derived from the local frequency of the visual words. Experimental results on a variety of examples demonstrate that the presented approach has the ability to quickly and intuitively visualize DNA sequences, and to help the user identify regions of differences among multiple datasets.
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_________::c995b5dfe9c4d2fea4c77bb928b69835 https://doi.org/10.1631/jzus.c1000091 Zobrazit plný text záznamu