Introduction

Graphical representations of contrasts in GC usage among codon frame positions (frame analysis) provide evidence of genes missing from the annotations of prokaryotic genomes of high GC content but the qualitative approach of visual frame analysis prevents its applicability on a genomic scale.We developed two quantitative methods for the identification and statistical characterization in sequence regions of three-base periodicity (hits) associated with open reading frame structures. The methods were implemented in the N-Profile Analysis Computational Tool (NPACT), which highlights in graphical representations inconsistencies between newly identified ORFs and pre-existing annotations of coding-regions. We applied the NPACT procedures to two recently annotated strains of the deltaproteobacterium Anaeromyxobacter dehalogenans, identifying in both genomes numerous conserved ORFs not included in the published annotation of coding regions.NPACT is available as a web-based service and for download at http://genome.ufl.edu/npact.lucianob@ufl.eduSupplementary data are available at Bioinformatics online.

Publications

  1. Quantitative frame analysis and the annotation of GC-rich (and other) prokaryotic genomes. An application to Anaeromyxobacter dehalogenans.
    Cite this
    Oden S, Brocchieri L, 2015-10-01 - Bioinformatics (Oxford, England)

Credits

  1. Steve Oden
    Developer

    Department of Molecular Genetics and Microbiology, University of Florida, United States of America

  2. Luciano Brocchieri
    Investigator

    Department of Molecular Genetics and Microbiology, University of Florida, United States of America

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Summary
AccessionBT006970
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByLuciano Brocchieri