BACTERIAL GENOMES
Associations Between Inverted Repeats and the Structural Evolution of Bacterial Genomes
... of bacterial genomes is challenged by recombination ...in bacterial genomes and their relation to the conservation of chromosomal ...the genomes. Closely related genomes reported ...
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Insertion sequence elements-mediated structural variations in bacterial genomes
... in bacterial genomes and play a crucial role in mediating large-scale variations in bacterial ...five bacterial species containing IS elements, including four strains of the ...different ...
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Periodic Variation of Mutation Rates in Bacterial Genomes Associated with Replication Timing
... genomes like those of Vibrio species require the additional firing of oriC2, which generates another burst of dNTP synthesis (Fig. 6C and D). Consequently, fast-growing bacteria may experience multiple pulses of ...
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Looking Backward To Move Forward: the Utility of Sequencing Historical Bacterial Genomes
... Historical bacterial genomes represent a unique source of genetic information and advancements in sequencing technologies have allowed unprecedented insights from this previously understudied ...historical ...
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Thousands of missed genes found in bacterial genomes and their analysis with COMBREX
... in bacterial genomes, revealing that, although the great majority of genes are found in every genome, a large number of very likely genes have been missed ...
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Weakly Deleterious Mutations and Low Rates of Recombination Limit the Impact of Natural Selection on Bacterial Genomes
... in bacterial genomes tend to cluster together (37), the variation in diversity could reflect stronger selection on synonymous codons in highly expressed genes, so that they have fewer effectively neu- tral ...
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Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes
... In bacterial genomes, they play a major role in the comings and goings of mobile genetic elements (MGEs), such as temperate phage genomes, integrated conjugative elements (ICEs) or integron ...
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The organization of bacterial genomes: towards understanding the interplay between structure and function
... organizing genomes in ...[1]. Bacterial H-NS-family pro- teins, SMC proteins, and eukaryotic insulator proteins bridge DNA to form loops at different length scales [2e ...understanding bacterial ...
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LAF: Logic Alignment Free and its application to bacterial genomes classification
... 1964 bacterial genomes from the NCBI genomes database ...(1964 bacterial genomes, 1157 species, 590 genera, 120 orders, 57 classes, and 36 ...
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Two-dimensional DNA displays for comparisons of bacterial genomes
... two-dimensional bacterial genomic display (2DBGD) was developed using restriction enzyme fragmentation to separate genomic DNA based on size, and then employing denaturing gradient gel electrophoresis (DGGE) in ...
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Comparison of long read sequencing technologies in the hybrid assembly of complex bacterial genomes
... genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome ...complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid ...
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Discovering Complete Quasispecies in Bacterial Genomes
... We extracted REPIN populations from 10 bacterial genomes in the following manner: For each of the genomes we deter- mined the most common 25-bp-long sequence. We then re- cursively searched the ...
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CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes
... many bacterial genomes with limited cost and labor, compared to previous ...by bacterial species harboring more than one replicon, which are not contemplated by the currently available ...of ...
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Inference of the Properties of the Recombination Process from Whole Bacterial Genomes
... in bacterial population genetics is biased recombina- tion, which we define in contrast to free recombination where all individuals in the population are equally likely to ...many bacterial populations imply ...
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Comparison of long read sequencing technologies in the hybrid assembly of complex bacterial genomes
... genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome ...complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid ...
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Evaluating genome dynamics: the constraints on rearrangements within bacterial genomes
... Most bacterial genomes contain multiple copies of some highly expressed genes (such as rrn genes) or have multiple copies of inser- tion sequences, ...as genomes diverge by nucleotide ...rearranged ...
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New players in the same old game: a system level in silico study to predict type III secretion system and effector proteins in bacterial genomes reveals common themes in T3SS mediated pathogenesis
... We have used BLAST (2.2.26 release) for searching homo- logues of T3SS components against the bacteria genomes [16]. We used ‘tblastn’ algorithm, which is a tool that com- pares a protein query sequence against a ...
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Genomes in space and time : insights into the functional three dimensional organization of prokaryotic and eukaryotic genomes in response to environmental stimuli and cell cycle progression : a thesis presented in partial fulfilment of the requirements for the degree of Doctorate in Philosophy in Genetics at Massey University, Albany, New Zealand
... eukaryotic genomes into multiple linear chromosomes results in four major challenges related to the regulation of chromosome replication and segregation, not encountered in circular bacterial ...
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Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries
... them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition ...5,203 bacterial genomes from 1,457 environmental metagenomic ...
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Natural diversity of cellulases, xylanases, and chitinases in bacteria
... sequenced bacterial genomes, the presence of GHs is mostly conserved at the genus level [7, 9]; therefore, the presence of GH domains in new members of previ- ously identified genera can be easily ...(i.e., ...
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