Literature DB >> 17077098

GECO--linear visualization for comparative genomics.

C T Kuenne1, R Ghai, T Chakraborty, T Hain.   

Abstract

UNLABELLED: In order to understand and interpret phylogenetic and functional relationships between multiple prokaryotic species, qualitative and quantitative data must be correlated and displayed. GECO allows linear visualization of multiple genomes using a client/server based approach by dynamically creating .png- or .pdf-formatted images. It is able to display ortholog relations calculated using BLASTCLUST by color coding ortholog representations. Irregularities on the genomic level can be identified by anomalous G/C composition. Thus, this software will enable researchers to detect horizontally transferred genes, pseudogenes and insertions/deletions in related microbial genomes. AVAILABILITY: http://bioinfo.mikrobio.med.uni-giessen.de/geco2/GecoMainServlet

Mesh：

Year:  2006        PMID： 17077098     DOI： 10.1093/bioinformatics/btl556

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


  16 in total

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Authors:  Martin Krzywinski; Jacqueline Schein; Inanç Birol; Joseph Connors; Randy Gascoyne; Doug Horsman; Steven J Jones; Marco A Marra
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3.  Complete sequences of plasmids from the hemolytic-uremic syndrome-associated Escherichia coli strain HUSEC41.

Authors:  Carsten Künne; Andre Billion; Stephen E Mshana; Judith Schmiedel; Eugen Domann; Hamid Hossain; Torsten Hain; Can Imirzalioglu; Trinad Chakraborty
Journal:  J Bacteriol       Date:  2012-01       Impact factor: 3.490

4.  Maltose and maltodextrin utilization by Listeria monocytogenes depend on an inducible ABC transporter which is repressed by glucose.

Authors:  Shubha Gopal; Daniela Berg; Nicole Hagen; Eva-Maria Schriefer; Regina Stoll; Werner Goebel; Jürgen Kreft
Journal:  PLoS One       Date:  2010-04-27       Impact factor: 3.240

5.  Comparative analysis of plasmids in the genus Listeria.

Authors:  Carsten Kuenne; Sonja Voget; Jordan Pischimarov; Sebastian Oehm; Alexander Goesmann; Rolf Daniel; Torsten Hain; Trinad Chakraborty
Journal:  PLoS One       Date:  2010-09-02       Impact factor: 3.240

6.  EDGAR 2.0: an enhanced software platform for comparative gene content analyses.

Authors:  Jochen Blom; Julian Kreis; Sebastian Spänig; Tobias Juhre; Claire Bertelli; Corinna Ernst; Alexander Goesmann
Journal:  Nucleic Acids Res       Date:  2016-04-20       Impact factor: 16.971

7.  Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes.

Authors:  Torsten Hain; Rohit Ghai; André Billion; Carsten Tobias Kuenne; Christiane Steinweg; Benjamin Izar; Walid Mohamed; Mobarak Abu Mraheil; Eugen Domann; Silke Schaffrath; Uwe Kärst; Alexander Goesmann; Sebastian Oehm; Alfred Pühler; Rainer Merkl; Sonja Vorwerk; Philippe Glaser; Patricia Garrido; Christophe Rusniok; Carmen Buchrieser; Werner Goebel; Trinad Chakraborty
Journal:  BMC Genomics       Date:  2012-04-24       Impact factor: 3.969

8.  Universal stress proteins are important for oxidative and acid stress resistance and growth of Listeria monocytogenes EGD-e in vitro and in vivo.

Authors:  Christa Seifart Gomes; Benjamin Izar; Farhad Pazan; Walid Mohamed; Mobarak Abu Mraheil; Krishnendu Mukherjee; André Billion; Yair Aharonowitz; Trinad Chakraborty; Torsten Hain
Journal:  PLoS One       Date:  2011-09-30       Impact factor: 3.240

9.  FdeC, a novel broadly conserved Escherichia coli adhesin eliciting protection against urinary tract infections.

Authors:  Barbara Nesta; Glen Spraggon; Christopher Alteri; Danilo Gomes Moriel; Roberto Rosini; Daniele Veggi; Sara Smith; Isabella Bertoldi; Ilaria Pastorello; Ilaria Ferlenghi; Maria Rita Fontana; Gad Frankel; Harry L T Mobley; Rino Rappuoli; Mariagrazia Pizza; Laura Serino; Marco Soriani
Journal:  MBio       Date:  2012-04-10       Impact factor: 7.867

10.  Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome.

Authors:  Carsten Kuenne; André Billion; Mobarak Abu Mraheil; Axel Strittmatter; Rolf Daniel; Alexander Goesmann; Sukhadeo Barbuddhe; Torsten Hain; Trinad Chakraborty
Journal:  BMC Genomics       Date:  2013-01-22       Impact factor: 3.969
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