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Nucleic Acids Research, 2003, Vol. 31, No. 13 3527-3532
© 2003 Oxford University Press

EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae

Liliana Florea*, Michael McClelland1, Cathy Riemer2, Scott Schwartz2 and Webb Miller2

Informatics Research, Celera/Applied Biosystems, 45 W. Gude Drive, Rockville, MD 20850, USA 1 Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, CA 92121, USA 2 Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA

*To whom correspondence should be addressed. Tel: +1 240 453 3736; Fax: +1 240 453 3324; Email: liliana.florea{at}celera.com

We describe EnteriX, a suite of three web-based visualization tools for graphically portraying alignment information from comparisons among several fixed and user-supplied sequences from related enterobacterial species, anchored on a reference genome (http://bio.cse.psu.edu/). The first visualization, Enteric, displays stacked pairwise alignments between a reference genome and each of the related bacteria, represented schematically as PIPs (Percent Identity Plots). Encoded in the views are large-scale genomic rearrangement events and functional landmarks. The second visualization, Menteric, computes and displays 1 Kb views of nucleotide-level multiple alignments of the sequences, together with annotations of genes, regulatory sites and conserved regions. The third, a Java-based tool named Maj, displays alignment information in two formats, corresponding roughly to the Enteric and Menteric views, and adds zoom-in capabilities. The uses of such tools are diverse, from examining the multiple sequence alignment to infer conserved sites with potential regulatory roles, to scrutinizing the commonalities and differences between the genomes for pathogenicity or phylogenetic studies. The EnteriX suite currently includes >15 enterobacterial genomes, generates views centered on four different anchor genomes and provides support for including user sequences in the alignments.


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