Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (2152K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (23)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Florea, L.
Right arrow Articles by McClelland, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Florea, L.
Right arrow Articles by McClelland, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2000, Vol. 28, No. 18 3486-3496
© 2000 Oxford University Press

Web-based visualization tools for bacterial genome alignments

Liliana Florea, Cathy Riemer, Scott Schwartz, Zheng Zhang, Nikola Stojanovic, Webb Miller* and Michael McClelland1

Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA and 1Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, CA 92121, USA

With the increase in the flow of sequence data, both in contigs and whole genomes, visual aids for comparison and analysis studies are becoming imperative. We describe three web-based tools for visualizing alignments of bacterial genomes. The first, called Enteric, produces a graphical, hypertext view of pairwise alignments between a reference genome and sequences from each of several related organisms, covering 20 kb around a user-specified position. Insertions, deletions and rearrangements relative to the reference genome are color-coded, which reveals many intriguing differences among genomes. The second, Menteric, computes and displays nucleotide-level multiple alignments of the same sequences, together with annotations of ORFs and regulatory sites, in a 1 kb region surrounding a given address. The third, a Java-based viewer called Maj, combines some features of the previous tools, and adds a zoom-in mechanism. We compare the Escherichia coli K-12 genome with the partially sequenced genomes of Klebsiella pneumoniae, Yersinia pestis, Vibrio cholerae, and the Salmonella enterica serovars Typhimurium, Typhi and Paratyphi A. Examination of the pairwise and multiple alignments in a region allows one to draw inferences about regulatory patterns and functional assignments. For example, these tools revealed that rffH, a gene involved in enterobacterial common antigen (ECA) biosynthesis, is partly deleted in one of the genomes. We used PCR to show that this deletion occurs sporadically in some strains of some serovars of S.enterica subspecies I but not in any strains tested from six other subspecies. The resulting cell surface diversity may be associated with selection by the host immune response.

* To whom correspondence should be addressed. Tel: +1 814 865 4551; Fax: +1 814 865 3176; Email: webb@bio.cse.psu.edu Present addresses: Zheng Zhang, Paracel Inc., Pasadena, CA 91101, USA Nikola Stojanovic, Whitehead Institute/MIT Center for Genome Research, Cambridge, MA 02141, USA


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Bacteriol.Home page
A. Boulanger, A. Francez-Charlot, A. Conter, M.-P. Castanie-Cornet, K. Cam, and C. Gutierrez
Multistress Regulation in Escherichia coli: Expression of osmB Involves Two Independent Promoters Responding either to {sigma}S or to the RcsCDB His-Asp Phosphorelay
J. Bacteriol., May 1, 2005; 187(9): 3282 - 3286.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. H. Sibley and E. A. Raleigh
Cassette-like variation of restriction enzyme genes in Escherichia coli C and relatives
Nucleic Acids Res., January 26, 2004; 32(2): 522 - 534.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. Herron-Olson, J. Freeman, Q. Zhang, E. F. Retzel, and V. Kapur
MGView: an alignment and visualization tool to enhance gap closure of microbial genomes
Nucleic Acids Res., September 1, 2003; 31(17): e106 - e106.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
R. Sturny, K. Cam, C. Gutierrez, and A. Conter
NhaR and RcsB Independently Regulate the osmCp1 Promoter of Escherichia coli at Overlapping Regulatory Sites
J. Bacteriol., August 1, 2003; 185(15): 4298 - 4304.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. Florea, M. McClelland, C. Riemer, S. Schwartz, and W. Miller
EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae
Nucleic Acids Res., July 1, 2003; 31(13): 3527 - 3532.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
O. Couronne, A. Poliakov, N. Bray, T. Ishkhanov, D. Ryaboy, E. Rubin, L. Pachter, and I. Dubchak
Strategies and Tools for Whole-Genome Alignments
Genome Res., January 1, 2003; 13(1): 73 - 80.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. D. Wilson, C. Riemer, D. W. Martindale, P. Schnupf, A. P. Boright, T. L. Cheung, D. M. Hardy, S. Schwartz, S. W. Scherer, L.-C. Tsui, et al.
Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5
Nucleic Acids Res., March 15, 2001; 29(6): 1352 - 1365.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. McClelland, L. Florea, K. Sanderson, S. W. Clifton, J. Parkhill, C. Churcher, G. Dougan, R. K. Wilson, and W. Miller
Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three Salmonella enterica serovars, Typhimurium, Typhi and Paratyphi
Nucleic Acids Res., December 15, 2000; 28(24): 4974 - 4986.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.