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Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria.

Glasner JD, Plunkett G, Anderson BD, Baumler DJ, Biehl BS, Burland V, Cabot EL, Darling AE, Mau B, Neeno-Eckwall EC, Pot D, Qiu Y, Rissman AI, Worzella S, Zaremba S, Fedorko J, Hampton T, Liss P, Rusch M, Shaker M, Shaull L, Shetty P, Thotakura S, Whitmore J, Blattner FR, Greene JM, Perna NT - Nucleic Acids Res. (2007)

Bottom Line: These organisms are increasingly the focus of studies using high-throughput experimental technologies and computational approaches.This wealth of data provides unprecedented opportunities for understanding the workings of basic biological systems and discovery of novel targets for development of vaccines, diagnostics and therapeutics.ERIC brings information together from disparate sources and supports data comparison across different organisms, analysis of varying data types and visualization of analyses in human and computer-readable formats.

View Article: PubMed Central - PubMed

Affiliation: Genome Center, University of Wisconsin, 425G Henry Mall, Madison, Madison, WI 53703, USA. jglasner@wisc.edu

ABSTRACT
ERIC, the Enteropathogen Resource Integration Center (www.ericbrc.org), is a new web portal serving as a rich source of information about enterobacteria on the NIAID established list of Select Agents related to biodefense-diarrheagenic Escherichia coli, Shigella spp., Salmonella spp., Yersinia enterocolitica and Yersinia pestis. More than 30 genomes have been completely sequenced, many more exist in draft form and additional projects are underway. These organisms are increasingly the focus of studies using high-throughput experimental technologies and computational approaches. This wealth of data provides unprecedented opportunities for understanding the workings of basic biological systems and discovery of novel targets for development of vaccines, diagnostics and therapeutics. ERIC brings information together from disparate sources and supports data comparison across different organisms, analysis of varying data types and visualization of analyses in human and computer-readable formats.

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Related in: MedlinePlus

Two views of the same region of the Mauve 2.0 alignment of 6 E. coli genomes. The visualization on the left uses the default color scheme based on homologous segments. Each color represents a collinear block that contains regions of homologous sequence. Importantly, islands unique to a single genome or collinear islands common to a subset of genomes are indicated. The visualization of the same aligned region shown on the right is colorized by multiplicity. Here, pink blocks indicate that the region is conserved across all six genomes. Other colors mark regions found in a subset of genomes.
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Figure 1: Two views of the same region of the Mauve 2.0 alignment of 6 E. coli genomes. The visualization on the left uses the default color scheme based on homologous segments. Each color represents a collinear block that contains regions of homologous sequence. Importantly, islands unique to a single genome or collinear islands common to a subset of genomes are indicated. The visualization of the same aligned region shown on the right is colorized by multiplicity. Here, pink blocks indicate that the region is conserved across all six genomes. Other colors mark regions found in a subset of genomes.

Mentions: Multiple genome alignments are available for each species of enterobacteria represented in ERIC–BRC (Figure 1). These alignments were constructed using a newly released progressive alignment tool, Mauve 2.0 (8,9), that dramatically improves alignment in regions conserved among subsets of genomes, a particularly important feature for recognition of genomic islands. This new version has significantly improved visualization and navigational tools and provides a powerful mechanism for comparative genomics of bacterial genomes.Figure 1.


Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria.

Glasner JD, Plunkett G, Anderson BD, Baumler DJ, Biehl BS, Burland V, Cabot EL, Darling AE, Mau B, Neeno-Eckwall EC, Pot D, Qiu Y, Rissman AI, Worzella S, Zaremba S, Fedorko J, Hampton T, Liss P, Rusch M, Shaker M, Shaull L, Shetty P, Thotakura S, Whitmore J, Blattner FR, Greene JM, Perna NT - Nucleic Acids Res. (2007)

Two views of the same region of the Mauve 2.0 alignment of 6 E. coli genomes. The visualization on the left uses the default color scheme based on homologous segments. Each color represents a collinear block that contains regions of homologous sequence. Importantly, islands unique to a single genome or collinear islands common to a subset of genomes are indicated. The visualization of the same aligned region shown on the right is colorized by multiplicity. Here, pink blocks indicate that the region is conserved across all six genomes. Other colors mark regions found in a subset of genomes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238966&req=5

Figure 1: Two views of the same region of the Mauve 2.0 alignment of 6 E. coli genomes. The visualization on the left uses the default color scheme based on homologous segments. Each color represents a collinear block that contains regions of homologous sequence. Importantly, islands unique to a single genome or collinear islands common to a subset of genomes are indicated. The visualization of the same aligned region shown on the right is colorized by multiplicity. Here, pink blocks indicate that the region is conserved across all six genomes. Other colors mark regions found in a subset of genomes.
Mentions: Multiple genome alignments are available for each species of enterobacteria represented in ERIC–BRC (Figure 1). These alignments were constructed using a newly released progressive alignment tool, Mauve 2.0 (8,9), that dramatically improves alignment in regions conserved among subsets of genomes, a particularly important feature for recognition of genomic islands. This new version has significantly improved visualization and navigational tools and provides a powerful mechanism for comparative genomics of bacterial genomes.Figure 1.

Bottom Line: These organisms are increasingly the focus of studies using high-throughput experimental technologies and computational approaches.This wealth of data provides unprecedented opportunities for understanding the workings of basic biological systems and discovery of novel targets for development of vaccines, diagnostics and therapeutics.ERIC brings information together from disparate sources and supports data comparison across different organisms, analysis of varying data types and visualization of analyses in human and computer-readable formats.

View Article: PubMed Central - PubMed

Affiliation: Genome Center, University of Wisconsin, 425G Henry Mall, Madison, Madison, WI 53703, USA. jglasner@wisc.edu

ABSTRACT
ERIC, the Enteropathogen Resource Integration Center (www.ericbrc.org), is a new web portal serving as a rich source of information about enterobacteria on the NIAID established list of Select Agents related to biodefense-diarrheagenic Escherichia coli, Shigella spp., Salmonella spp., Yersinia enterocolitica and Yersinia pestis. More than 30 genomes have been completely sequenced, many more exist in draft form and additional projects are underway. These organisms are increasingly the focus of studies using high-throughput experimental technologies and computational approaches. This wealth of data provides unprecedented opportunities for understanding the workings of basic biological systems and discovery of novel targets for development of vaccines, diagnostics and therapeutics. ERIC brings information together from disparate sources and supports data comparison across different organisms, analysis of varying data types and visualization of analyses in human and computer-readable formats.

Show MeSH
Related in: MedlinePlus