Literature DB >> 10980154

Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes.

A C Frank1, J R Lobry.   

Abstract

SUMMARY: A program called Oriloc has been developed for the prediction of bacterial replication origins. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. The program works with unannotated sequences in fasta format and therefore uses glimmer 2.0 outputs to discriminate between codon positions so as to increase the signal/noise ratio.

Mesh：

Year:  2000        PMID： 10980154     DOI： 10.1093/bioinformatics/16.6.560

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  56 in total

1.  Where does bacterial replication start? Rules for predicting the oriC region.

Authors:  Pawel Mackiewicz; Jolanta Zakrzewska-Czerwinska; Anna Zawilak; Miroslaw R Dudek; Stanislaw Cebrat
Journal:  Nucleic Acids Res       Date:  2004-07-16       Impact factor: 16.971

2.  Complete nucleotide sequence analysis of plasmids in strains of Staphylococcus aureus clone USA300 reveals a high level of identity among isolates with closely related core genome sequences.

Authors:  Adam D Kennedy; Stephen F Porcella; Craig Martens; Adeline R Whitney; Kevin R Braughton; Liang Chen; Carly T Craig; Fred C Tenover; Barry N Kreiswirth; James M Musser; Frank R DeLeo
Journal:  J Clin Microbiol       Date:  2010-10-13       Impact factor: 5.948

3.  Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts.

Authors:  Xiaodong Bai; Jianhua Zhang; Adam Ewing; Sally A Miller; Agnes Jancso Radek; Dmitriy V Shevchenko; Kiryl Tsukerman; Theresa Walunas; Alla Lapidus; John W Campbell; Saskia A Hogenhout
Journal:  J Bacteriol       Date:  2006-05       Impact factor: 3.490

4.  Evolutionary constraints on codon and amino acid usage in two strains of human pathogenic actinobacteria Tropheryma whipplei.

Authors:  Sabyasachi Das; Sandip Paul; Chitra Dutta
Journal:  J Mol Evol       Date:  2006-03-22       Impact factor: 2.395

5.  Genome sequence analysis of the emerging human pathogenic acetic acid bacterium Granulibacter bethesdensis.

Authors:  David E Greenberg; Stephen F Porcella; Adrian M Zelazny; Kimmo Virtaneva; Dan E Sturdevant; John J Kupko; Kent D Barbian; Amenah Babar; David W Dorward; Steven M Holland
Journal:  J Bacteriol       Date:  2007-09-07       Impact factor: 3.490

6.  Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides.

Authors:  Paul J McMurdie; Sebastian F Behrens; Jochen A Müller; Jonathan Göke; Kirsti M Ritalahti; Ryan Wagner; Eugene Goltsman; Alla Lapidus; Susan Holmes; Frank E Löffler; Alfred M Spormann
Journal:  PLoS Genet       Date:  2009-11-06       Impact factor: 5.917

7.  Non mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus.

Authors:  Fabienne Ripoll; Sophie Pasek; Chantal Schenowitz; Carole Dossat; Valérie Barbe; Martin Rottman; Edouard Macheras; Beate Heym; Jean-Louis Herrmann; Mamadou Daffé; Roland Brosch; Jean-Loup Risler; Jean-Louis Gaillard
Journal:  PLoS One       Date:  2009-06-19       Impact factor: 3.240

8.  A study in entire chromosomes of violations of the intra-strand parity of complementary nucleotides (Chargaff's second parity rule).

Authors:  B R Powdel; Siddhartha Sankar Satapathy; Aditya Kumar; Pankaj Kumar Jha; Alak Kumar Buragohain; Munindra Borah; Suvendra Kumar Ray
Journal:  DNA Res       Date:  2009-10-27       Impact factor: 4.458

9.  The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection.

Authors:  Kazuharu Arakawa; Masaru Tomita
Journal:  Evol Bioinform Online       Date:  2007-09-06       Impact factor: 1.625

10.  Adaptation of the short intergenic spacers between co-directional genes to the Shine-Dalgarno motif among prokaryote genomes.

Authors:  Albert Pallejà; Santiago García-Vallvé; Antoni Romeu
Journal:  BMC Genomics       Date:  2009-11-18       Impact factor: 3.969
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