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BOSC 2008 Lightning Talk: The E nteropathogen R esource I ntegration C enter (ERIC), A NIAID Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Disease http://www.ericbrc.org D. Pot 1 , J. Whitmore 1 , M. Shaker 1 , J. Fedorko 1 , K. Joshi 1 , S. Nanan 1 , P. Shetty 1 , J. Thangiah 1 , S. Zaremba 1 , G. Plunkett, III 2 , J. Glasner 2 , B. Anderson 2 , D. Baumler 2 , B. Biehl 2 , V. Burland 2 , E. Cabot 2 , E. Neeno-Eckwall 2 , B. Mau 2 , P. Liss 2 , M. Rusch 2 , F. R. Blattner 2 , N. T. Perna 2 , J. M. Greene 1 1 SRA International, Inc., Rockville MD and 2 University of Wisconsin, Madison WI
ERIC is a NIAID Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Disease , one of 8 such centers funded in July 2004 for 5 years.
ERIC primarily focuses on the integration of data from five enteropathogens as well as related reference organisms:
Diarrheagenic E. coli
Partnership between personnel at the Genome Center of Wisconsin (Nicole Perna, Fred Blattner, Guy Plunkett) and SRA International’s Global Health Sector, Rockville MD.
Everything done under contract funding required to be made freely available to the Scientific Community.
ERIC-Overview Genomes Annotations (ASAP) Genome Views and Comparisons (Mauve, GBrowse) Microarray Analysis (mAdb) ERIC is a portal based system using the JBoss portal . ASAP ( A Systematic Annotation Package for community annotation) from UW-Madison is being used to allow the scientific community to annotate genes for the five enteropathogens and related reference organism useful for comparative genomics.
ERIC contains tools for comparative genomics, such as Mauve, which has the distinct advantage of allowing comparison of more than two genomes, as well as being able to handle chromosomal rearrangements. (We provide access to some other pathogenic and non-pathogenic reference genomes, particularly for E. coli .)
Mauve identifies and aligns regions of local collinearity called locally collinear blocks (LCBs). Each locally collinear block is a homologous region of sequence shared by two or more of the genomes under study, and does not contain any rearrangements
of homologous sequence.
The Mauve genome alignment procedure results in a global alignment of each locally collinear block that has sequence elements conserved among all the genomes under study. Nucleotides in any given genome are aligned only once to other genomes,
suggesting orthology among aligned residues. Mauve makes no attempt to align paralogous regions.
The remaining unaligned regions may be lineage-specific sequence or rearranged or paralogous repetitive regions and can be identified as such
during subsequent processing with other tools.
Available at: http://gel.ahabs.wisc.edu/mauve/download.php