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Robust classifying of prokaryotic genomes

Paper ID Volume ID Publish Year Pages File Format Full-Text
15176 1385 2012 10 PDF Available
Title
Robust classifying of prokaryotic genomes
Abstract

In this paper, we propose a method to classify prokaryotic genomes using the agglomerative information bottleneck method for unsupervised clustering. Although the method we present here is closely related to a group of methods based on detecting the presence or absence of genes, our method is different because it uses gene lengths as well. We show that this amended method is reliable. For robustness evaluation, we apply bootstrap and jackknife techniques to input data. As a result, we are able to propose an approach to determine the stability level of a cladogram. We demonstrate that the genome tree produced for a selected small group of genomes looks a lot like a phylogenetic tree of this group.

Graphical abstractFigure optionsDownload full-size imageDownload as PowerPoint slideHighlights► We present a method of genome clustering using information bottleneck approach. ► Resulted dendrograms are strongly similar to corresponding phylogenetic trees. ► We estimate the robustness of the method proposed by us. ► We show that jackknifing is functional to determine stability of genome classification. ► We conclude that usage of a preprocessing filtering parameter is valuable.

Keywords
IB, information bottleneck; COGs, clusters of orthologous groups; UPGMA, unweighted pair group method with arithmetic mean; NJ, neighbor joining methodAgglomerative clustering; Information bottleneck method; Jackknifing; Gene length; Phylogenomics
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 40, October 2012, Pages 20–29
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us