Abstract
The genomes of living organisms are populated with pleomorphic repetitive elements (REs) of varying densities. Our hypothesis that genomic RE landscapes are species/strain/individual-specific was implemented into the Genome Signature Imaging system to visualize and compute the RE-based signatures of any genome. Following the occurrence profiling of 5-nucleotide REs/words, the information from top-50 frequency words was transformed into a genome-specific signature and visualized as Genome Signature Images (GSIs), using a CMYK scheme. An algorithm for computing distances among GSIs was formulated using the GSIs' variables (word identity, frequency, and frequency order). The utility of the GSI-distance computation system was demonstrated with control genomes. GSI-based computation of genome-relatedness among 1766 microbes (117 archaea and 1649 bacteria) identified their clustering patterns; although the majority paralleled the established classification, some did not. The Genome Signature Imaging system, with its visualization and distance computation functions, enables genome-scale evolutionary studies involving numerous genomes with varying sizes.
Original language | English (US) |
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Pages (from-to) | 30-42 |
Number of pages | 13 |
Journal | Genomics |
Volume | 106 |
Issue number | 1 |
DOIs | |
State | Published - Jul 1 2015 |
Keywords
- Genome distance
- Genome signature
- Genome visualization
- Genome-scale classification
- Microbial genomes
- Repetitive element
ASJC Scopus subject areas
- Genetics