GraphDNA: a Java program for graphical display of DNA composition analyses.
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TLDR
GraphDNA is a platform-independent, Open Source tool for the analysis of nucleotide trends in DNA sequences that displays multiple DNA nucleotide composition graphs (skews and walks) in a single window to allow direct comparisons between the sequences.Abstract:
Under conditions of no strand bias the number of Gs is equal to that of Cs for each DNA strand; similarly, the total number of Ts is equal to that of As. However, within each strand there are considerable local deviations from the A = T and G = C equality. These asymmetries in nucleotide composition have been extensively analyzed in prokaryotic and eukaryotic genomes and related to chromosome organization, transcription orientation and other processes in certain organisms. To carry out analysis of intra-strand nucleotide distribution several graphical methods have been developed. GraphDNA is a new Java application that provides a simple, user-friendly interface for the visualization of DNA nucleotide composition. The program accepts GenBank, EMBL and FASTA files as an input, and it displays multiple DNA nucleotide composition graphs (skews and walks) in a single window to allow direct comparisons between the sequences. We illustrate the use of DNA skews for characterization of poxvirus and coronavirus genomes. GraphDNA is a platform-independent, Open Source, tool for the analysis of nucleotide trends in DNA sequences. Multiple sequence formats can be read and multiple sequences may be plotted in a single results window.read more
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iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC
TL;DR: Rigorous cross validations on the benchmark datasets from four yeast species have indicated that the proposed predictor is really very powerful for predicting the entire DNA duplication origins of yeast species.
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The mitochondrial genome of Paraminabea aldersladei (Cnidaria: Anthozoa: Octocorallia) supports intramolecular recombination as the primary mechanism of gene rearrangement in octocoral mitochondrial genomes.
TL;DR: Mapping the distribution of mt gene arrangements onto a taxonomically comprehensive phylogeny of Octocorallia suggests that all of the known octocoral gene orders have evolved by successive inversions of one or more evolutionarily conserved blocks of protein-coding genes.
Journal ArticleDOI
The mitochondrial genome of a deep-sea bamboo coral (Cnidaria, Anthozoa, Octocorallia, Isididae): genome structure and putative origins of replication are not conserved among octocorals.
TL;DR: Comparative analyses suggest that intramitochondrial recombination and errors in replication at OriH may be responsible for changes in gene order in octocorals and hexacorals, respectively and no evidence for strand-specific mutational biases that may influence phylogenetic analyses that include this subfamily of bamboo corals is found.
Journal ArticleDOI
Genome Sequence of Thermofilum pendens Reveals an Exceptional Loss of Biosynthetic Pathways without Genome Reduction
Iain Anderson,Jason R. Rodriguez,Dwi Susanti,Dwi Susanti,Iris Porat,Claudia I. Reich,Luke E. Ulrich,James Elkins,Kostas Mavromatis,Athanasios Lykidis,Edwin Kim,Linda S. Thompson,Linda S. Thompson,Matt Nolan,Miriam Land,Alex Copeland,Alla Lapidus,Susan Lucas,Chris Detter,Chris Detter,Igor B. Zhulin,Gary J. Olsen,William B. Whitman,Biswarup Mukhopadhyay,James Bristow,Nikos C. Kyrpides +25 more
TL;DR: The complete genome of Thermofilum pendens, a deeply branching, hyperthermophilic member of the order Thermoproteales in the archaeal kingdom Crenarchaeota, is reported, finding that T. pendens has adapted to life in an environment rich in nutrients.
Journal ArticleDOI
Identification of replication origins in prokaryotic genomes
TL;DR: The main existing approaches to the identification of replication origin (oriC) and termination (terC) loci in prokaryotic chromosomes are described and a number of computational tools based on various skew types and other types of evidence are characterized.
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Journal ArticleDOI
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Kim Rutherford,Julian Parkhill,James Crook,Terry Horsnell,Peter M. Rice,Marie-Adèle Rajandream,Bart Barrell +6 more
TL;DR: Artemis is a DNA sequence visualization and annotation tool that allows the results of any analysis or sets of analyses to be viewed in the context of the sequence and its six-frame translation.
Journal ArticleDOI
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TL;DR: The genome sequence reveals that the severe acute respiratory syndrome–associated coronavirus known as the Tor2 isolate is only moderately related to other known coronaviruses, andylogenetic analysis of the predicted viral proteins indicates that the virus does not closely resemble any of the three previously known groups of coronavirs.
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