EnteriX:
 
Visualization Tools for Bacterial Genome Alignments

The Computational Molecular Biology Group, Department of Computer Science and Engineering, Penn State University

This site allows comparative views of a reference genome (either E. coli K-12 or O157:H7, S. typhimurium LT2, S. typhi CT18 or S. paratyphi A) with sequences from several related bacteria using three different visualization tools. The Enteric server offers large-scale views of pairwise alignments, with point-and-click capabilities to retrieve related gene and alignment information. The Menteric tool displays nucleotide-level multiple alignments of the bacterial sequences, along with regulatory site annotations which the user interested in conservation and functional studies may want to explore further. The Maj viewer combines features of the previous two tools, and includes a zoom-in mechanism that allows examination both of the large-scale pairwise alignments and of the highest-scoring nucleotide-level multiple alignment in a sub-region selected by the user.

Each tool is accompanied by documentation on its features and provides links to related sites of potential interest, for easy navigation.
 

            The Enteric server

            The Menteric server

            The Maj viewer

A list of bibliographical references for these tools is here.

If you use this software in a publication, please cite:

• Nucleic Acids Research, 2000, Vol 28, No 18. "Web-based visualization tools for bacterial genome alignments." Liliana Florea, Cathy Riemer, Scott Schwartz, Zheng Zhang, Nikola Stojanovic, Webb Miller, Michael McClelland.
   
• Nucleic Acids Research, 2003, Vol 31, No 13. "Enterix 2003: visualization tools for genome alignments of enterobacteriaceae." Liliana Florea, Michael McClelland, Cathy Riemer, Scott Schwartz, Webb Miller.

Bacterial sequences used in comparative views

• The E. coli K-12 sequence was obtained from the Entrez Genomes section at NCBI. The annotations are according to Blattner et al. (1997).
   
• The sequence for the E. coli enterohemorrhagic strain O157:H7 EDL933 was obtained from the anonymous ftp site of the E. coli Genome Project at the University of Wisconsin, Madison.
   
• The complete sequence of the Salmonella typhimurium LT2 genome and annotations were obtained from the web site of the Genome Sequencing Center at Washington University, St. Louis.
   
• The genome sequence of S. paratyphi A and contig data for S. paratyphi B and for Klebsiella pneumoniae were downloaded from the web site of the Genome Sequencing Center at Washington University, St. Louis.
   
• Contig data for S. enteriditis and S. dublin were obtained from the Salmonella Sequence Server at the University of Illinois, Urbana Champaign.
   
• Contig data for S. enteriditis PT4, S. gallinarum and S. arizonae were downloaded from the Sanger Center's ftp site.
   
• Contig data for S. bongori and S. typhimurium SL1344 were obtained from the Salmonella sequence download site at the Sanger Center, UK.
   
• The complete sequence data for S. typhi were obtained from the web site of the Sanger Center, UK.
   
• The complete sequence data for Erwinia carotovora subspecies atroseptica SCRI1043 was downloaded from the Sanger Center ftp site.
   
• Partial sequences of Escherichia coli 042 and E2348, Shigella dysenteriae M131649 and Shigella sonnei 53G were downloaded from the ftp site at the Sanger Center.
   
• The complete sequence data for Yersinia pestis were obtained from the web site of the Sanger Center, UK.
   
• Partial sequences for Yersinia enterocolitica (type 0:8) were downloaded from the Sanger Center's ftp site.
   
• The complete sequence of the genome Pseudomonas aeruginosa strain PAO1 was obtained from the web site of the Pseudomonas Genome Center.