NDLI: Detection of Genomic Idiosyncrasies Using Fuzzy Phylogenetic Profiles

Content Provider	PubMed Central
Author	Psomopoulos, Fotis E. Mitkas, Pericles A. Ouzounis, Christos A.
Editor	Promponas, Vasilis J.
Copyright Year	2013
Abstract	Phylogenetic profiles express the presence or absence of genes and their homologs across a number of reference genomes. They have emerged as an elegant representation framework for comparative genomics and have been used for the genome-wide inference and discovery of functionally linked genes or metabolic pathways. As the number of reference genomes grows, there is an acute need for faster and more accurate methods for phylogenetic profile analysis with increased performance in speed and quality. We propose a novel, efficient method for the detection of genomic idiosyncrasies, i.e. sets of genes found in a specific genome with peculiar phylogenetic properties, such as intra-genome correlations or inter-genome relationships. Our algorithm is a four-step process where genome profiles are first defined as fuzzy vectors, then discretized to binary vectors, followed by a de-noising step, and finally a comparison step to generate intra- and inter-genome distances for each gene profile. The method is validated with a carefully selected benchmark set of five reference genomes, using a range of approaches regarding similarity metrics and pre-processing stages for noise reduction. We demonstrate that the fuzzy profile method consistently identifies the actual phylogenetic relationship and origin of the genes under consideration for the majority of the cases, while the detected outliers are found to be particular genes with peculiar phylogenetic patterns. The proposed method provides a time-efficient and highly scalable approach for phylogenetic stratification, with the detected groups of genes being either similar to their own genome profile or different from it, thus revealing atypical evolutionary histories.
Related Links	http://dx.doi.org/10.1371/journal.pone.0052854
Starting Page	52854
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	1
Volume Number	8
Language	English
Publisher	Public Library of Science
Publisher Date	2013-01-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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