Filters








29,561 Hits in 5.1 sec

Comparative genomics study of inverted repeats in bacteria [article]

Fabrizio Lillo, Salvatore Basile, Rosario N. Mantegna
2002 arXiv   pre-print
We investigate the number of inverted repeats observed in 37 complete genomes of bacteria.  ...  By using the information annotated in the genomes we discover that in most of the eubacteria the inverted repeats of stem length longer than 8 nucleotides preferentially locate near the 3' end of the nearest  ...  This work is part of the INFM-PAIS project "Statistical modeling of non-coding DNA".  ... 
arXiv:cond-mat/0105479v2 fatcat:fwpvif4v6rdn5euqkzqhgxio6y

Comparative genomics study of inverted repeats in bacteria

F. Lillo, S. Basile, R. N. Mantegna
2002 Bioinformatics  
We investigate the number of inverted repeats observed in 37 complete genomes of bacteria.  ...  DATA AND METHODS In the present study, we investigate 37 complete genomes of bacteria recently sequenced (all the bacterial complete genomes publicly available at the time of our study).  ...  This work is part of the INFM-PAIS project "Statistical modeling of non-coding DNA".  ... 
doi:10.1093/bioinformatics/18.7.971 pmid:12117795 fatcat:ysmmtgwaebfmtpwh6afxqq2pnq

The Excess of Small Inverted Repeats in Prokaryotes

Emmanuel D. Ladoukakis, Adam Eyre-Walker
2008 Journal of Molecular Evolution  
Recent analyses have shown that there is a large excess of perfect inverted repeats in many prokaryotic genomes but not in eukaryotic ones.  ...  When both methods are applied to bacterial protein coding sequences they both detect an excess of inverted repeats, which is much lower than previously reported in whole prokaryotic genomes.  ...  Recently, two studies investigated the impact of sequence-directed mutagenesis in the formation of short inverted repeats on a genomic scale.  ... 
doi:10.1007/s00239-008-9151-z pmid:18696026 fatcat:c2iyneuohjgt5dwcf7zl2oasty

The genome of lipid-containing bacteriophage PRD1, which infects gram-negative bacteria, contains long, inverted terminal repeats

D D Gerendasy, J Ito
1987 Journal of Virology  
We report here that the PRD1 genome contains a 111-base-pair terminal inverted repeat which does not bear homology to that of any known linear duplex DNAs with terminal proteins.  ...  The bacteriophage PRD1 is a lipid-bearing phage that infects a wide variety of gram-negative bacteria, including Escherichia coli and Salmonella typhimurium when they contain the appropriate plasmid.  ...  In this note, we report the existence of a 111-nucleotide terminal inverted repeat at the ends of the PRD1 genome.  ... 
doi:10.1128/jvi.61.2.594-596.1987 fatcat:mewefpai6nckjlzqmjbypgbjf4

The genome of lipid-containing bacteriophage PRD1, which infects gram-negative bacteria, contains long, inverted terminal repeats

D D Gerendasy, J Ito
1987 Journal of Virology  
We report here that the PRD1 genome contains a 111-base-pair terminal inverted repeat which does not bear homology to that of any known linear duplex DNAs with terminal proteins.  ...  The bacteriophage PRD1 is a lipid-bearing phage that infects a wide variety of gram-negative bacteria, including Escherichia coli and Salmonella typhimurium when they contain the appropriate plasmid.  ...  In this note, we report the existence of a 111-nucleotide terminal inverted repeat at the ends of the PRD1 genome.  ... 
pmid:3543400 pmcid:PMC253986 fatcat:lp4k3pm3c5d6fdtby5uhyap47i

Comparative genomics of pyridoxal 5′-phosphate-dependent transcription factor regulons in Bacteria

Inna A. Suvorova, Dmitry A. Rodionov
2016 Microbial Genomics  
To identify putative target genes and DNA binding motifs of MocR-TFs, we performed comparative genomics analysis of over 250 bacterial genomes.  ...  Motifs with direct and/or inverted repeat symmetry constitute the majority of inferred DNA motifs, suggesting preferable TF dimerization in head-to-tail or head-to-head configuration.  ...  Acknowledgements This work was supported by the Russian Foundation for Basic Research (14-04-00870, 14-04-91154) and by the Russian Academy of Sciences via the program 'Molecular and Cellular Biology'.  ... 
doi:10.1099/mgen.0.000047 pmid:28348826 pmcid:PMC5320631 fatcat:rnr5w7fhvzdexep42nxvyr4vbe

Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids

Richard P. Bowater, Natália Bohálová, Václav Brázda
2022 International Journal of Molecular Sciences  
We highlight that, in the majority of genomes, inverted repeats are present in higher numbers than is expected from a random occurrence.  ...  Inverted repeat sequences also influence the evolution of genomes, and growing evidence highlights their significance in several human diseases, suggesting that the inverted repeat sequences and/or DNA  ...  Prokaryotes Early evidence for the presence of inverted repeats and cruciforms in genomes was obtained from studies across a range of bacteria, with a particular focus on E. coli [6] .  ... 
doi:10.3390/ijms23116171 pmid:35682854 fatcat:mqmikhqoubg6fd6xinc3f3o6p4

DNA repeats lead to the accelerated loss of gene order in bacteria

Eduardo P.C. Rocha
2003 Trends in Genetics  
Large segment inversions tend to be caused by homologous recombination between inverted repeats, and most experimental studies use inverted repeats to produce large rearrangements [9] [10] [11] [12] .  ...  Conclusions Comparing the frequency of putative recombination events between different bacteria involves several simplifying assumptions.  ... 
doi:10.1016/j.tig.2003.09.011 pmid:14585609 fatcat:fylemkx4gbfv5dlom7enpgxni4

Effects of reunited diverged regulatory hierarchies in allopolyploids and species hybrids

Nicole C. Riddle, James A. Birchler
2003 Trends in Genetics  
Large segment inversions tend to be caused by homologous recombination between inverted repeats, and most experimental studies use inverted repeats to produce large rearrangements [9] [10] [11] [12] .  ...  Conclusions Comparing the frequency of putative recombination events between different bacteria involves several simplifying assumptions.  ... 
doi:10.1016/j.tig.2003.09.005 pmid:14585608 fatcat:2h5vyrzmq5gkrloe6gf54qelh4

Solving ambiguities in contig assembly ofIdiomarina loihiensisL2TR chromosome byin silicoanalyses

François Collyn, Claude-Alain H. Roten, Lionel Guy
2007 FEMS Microbiology Letters  
The presence of 3.4-kb inverted repeated sequences at the borders of the putative rearrangement supports this hypothesis.  ...  Reverting in silico this segment restores (1) a symmetric chromosome architecture; (2) the co-orientation of transcription of all rRNA operons with DNA replication; and (3) a better conservation of gene  ...  of I. lohiensis L2TR.  ... 
doi:10.1111/j.1574-6968.2007.00714.x pmid:17442016 fatcat:xiurq2r435fchhohoukb2hxtle

Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue

Hela El Kafsi, Valentin Loux, Mahendra Mariadassou, Camille Blin, Hélène Chiapello, Anne-Laure Abraham, Emmanuelle Maguin, Maarten van de Guchte
2017 Scientific Reports  
One very intriguing observation we made when resolving the first L. bulgaricus genome sequence was that of the presence of a 47.5 kbp inverted repeat (IR) in the replication terminus region 5 .  ...  The first Lactobacillus delbrueckii ssp. bulgaricus genome sequence revealed the presence of a very large inverted repeat (IR), a DNA sequence arrangement which thus far seemed inconceivable in a nonmanipulated  ...  from Genbank and analysed for the presence of large inverted repeats comparable to those found in the L. delbrueckii ssp. bulgaricus ATCC11842 genome 5 using Repseek 43 with the following parameters:  ... 
doi:10.1038/srep44331 pmid:28281695 pmcid:PMC5345009 fatcat:7wvzzygzjnhydpk3bn2kps4oie

Associations between inverted repeats and the structural evolution of bacterial genomes

Guillaume Achaz, Eric Coissac, Pierre Netter, Eduardo P C Rocha
2003 Genetics  
Closely related genomes reported to differ in terms of stability are also found to differ in the number of inverted repeats.  ...  ., inversions) are thought to frequently operate by homologous recombination between inverted repeats, we analyzed the presence and distribution of such repeats in bacterial genomes and their relation  ...  Given the lack of experimental comparative studies occurrences induce large changes.  ... 
pmid:12930739 pmcid:PMC1462642 fatcat:qqnudufwf5b6hbbexrkewnyaue

Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance

K. G. Lim, C. K. Kwoh, L. Y. Hsu, A. Wirawan
2012 Briefings in Bioinformatics  
The prevalence of tandem repeats in eukaryotic genomes and their association with a number of genetic diseases has raised considerable interest in locating these repeats.  ...  In this review, we have systematically separated the algorithmic aspect of the search tools from the influence of the parameter settings.  ...  In fact, repeats with period sizes beyond 6 bp account for at least half the total of number of repeats detected in the human genome, >60% of the three other eukaryotic species and >70% of the five bacteria  ... 
doi:10.1093/bib/bbs023 pmid:22648964 fatcat:q2h4imsbgjgttnwp2ijrvlky6a

Visualization and Significance of DNA Structural Motifs in the Campylobacter jejuni Genome

Lise Petersen, Stephen L. W. On, David W. Ussery
2002 Genome Letters  
Compared with the average, global repeats are underrepresented in C. jejuni, whereas local repeats are overrepresented and the percentage of palindromes exceeds that of most other pathogenic bacteria.  ...  In addition, we calculated the frequency of DNA repeats in C. jejuni and in chromosomes from 25 other species of the class Proteobacteria.  ...  Global repeats are less frequent in C. jejuni compared with the average of the other genomes (note in particular the very low levels of global inverted repeats; see Fig. 1a ).  ... 
doi:10.1166/gl.2002.004 fatcat:h4lkcxsnergfnb3rbokfjljh44

Characteristic enrichment of DNA repeats in different genomes

R. Cox, S. M. Mirkin
1997 Proceedings of the National Academy of Sciences of the United States of America  
By contrast, in all eukaryotic genomes studied, we observed an overrepresentation of all repeats, especially homopurine-homopyrimidine mirror repeats.  ...  Comparison of observed frequencies with expectations revealed that in bacterial genomes and organelles the frequency of different repeats is either random or enriched for inverted and͞or direct tandem  ...  As can be seen in these data, all types of repeats are overrepresented in eukaryotes, but only inverted and direct repeats are significant in organelles and at least some bacteria.  ... 
doi:10.1073/pnas.94.10.5237 pmid:9144221 pmcid:PMC24662 fatcat:5bksbpewnzhfhh4qjgusxxvz4e
« Previous Showing results 1 — 15 out of 29,561 results