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From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria
The rapid increase in published genomic sequences for bacteria presents the first opportunity to reconstruct evolutionary events on the scale of entire genomes. However, extensive lateral geneExpand
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Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs
  • E. Lerat
  • Biology, Medicine
  • Heredity
  • 1 June 2010
The production of genome sequences has led to another important advance in their annotation, which is closely linked to the exact determination of their content in terms of repeats, among which areExpand
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Evolutionary Origins of Genomic Repertoires in Bacteria
Explaining the diversity of gene repertoires has been a major problem in modern evolutionary biology. In eukaryotes, this diversity is believed to result mainly from gene duplication and loss, but inExpand
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The source of laterally transferred genes in bacterial genomes
BackgroundLaterally transferred genes have often been identified on the basis of compositional features that distinguish them from ancestral genes in the genome. These genes are usually A+T-rich,Expand
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The evolutionary history of quorum-sensing systems in bacteria.
Communication among bacterial cells through quorum-sensing (QS) systems is used to regulate ecologically and medically important traits, including virulence to hosts. QS is widespread in bacteria; itExpand
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Examining bacterial species under the specter of gene transfer and exchange
Even in lieu of a dependable species concept for asexual organisms, the classification of bacteria into discrete taxonomic units is considered to be obstructed by the potential for lateral geneExpand
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Recognizing the pseudogenes in bacterial genomes
Pseudogenes are now known to be a regular feature of bacterial genomes and are found in particularly high numbers within the genomes of recently emerged bacterial pathogens. As most pseudogenes areExpand
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Sequence divergence within transposable element families in the Drosophila melanogaster genome.
The availability of the sequenced Drosophila melanogaster genome provides an opportunity to study sequence variation between copies within transposable element families. In this study,we analyzed theExpand
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“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
BackgroundOf the different bioinformatic methods used to recover transposable elements (TEs) in genome sequences, one of the most commonly used procedures is the homology-based method proposed by theExpand
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UrQt: an efficient software for the Unsupervised Quality trimming of NGS data
TLDR
We present a new quality control method, implemented in UrQt software, for Unsupervised Quality trimming of Next Generation Sequencing reads. Expand
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