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ERIC News
  
Welcome to ERIC! - the Enteropathogen Resource Integration Center.

ERIC is one of eight Bioinformatics Resource Centers (BRC) for Biodefense and Emerging/Re-Emerging Infectious Diseases. Funded by the National Institute of Allergy and Infectious Diseases (NIAID), ERIC serves as an information resource for five members of the bacterial family Enterobacteriaceae.  

IMPORTANT NOTICE FOR ERIC USERS

ERIC will be ceasing operations by the end of February 2010. NIAID has awarded a contract to the Virginia Bioinformatics Institute(VBI) to create a consolidated BRC for all of the NIAID category A-C priority pathogenic bacteria. PATRIC's initial all-bacterial system is online now at http://patricbrc.vbi.vt.edu. We remain in the process of transitioning ERIC's data and software to PATRIC for incorporation into their new Web-based bioinformatics resource, and we suggest you check them out now and begin to familiarize yourself with their new site.

After ERIC ceases operations in February, almost all of our data will also be available at the University of Wisconsin-Madison's ASAP site, which will remain operational. It is located at http://www.genome.wisc.edu/tools/asap.htm

We thank all of ERIC's users and collaborators for the privilege of serving you over the past five and a half years.

New ERIC Tool for Producing Boolean Combinations of Gene Lists
ERIC has added a new tool to allow a user to create lists of genes by various filtering queries (Keyword, Subcellular Localization, Genes containing SNPs, and Virulence Genes) on the "Search" tab, and then if desired combine those lists in Boolean combinations on the "My Queries" tab, using AND, OR, or NOT.

For example, for a given strain one could ask for all genes containing SNPs (Query 1), then ask for all genes containing the keyword "iron transport" in the gene annotations (Query 2). Combining Queries 1 AND 2 would produce a resulting list of only those iron transport genes containing SNPs (Query 3). This resulting list (Query 3) could then be used in turn with other query list results and Boolean operators to filter the results in other ways.

This new Query Intersection tool can be found on the Genome Tools portlet at the right of the home page, as well as under the Genome Tools tab at the top of the home page.

Literature Text Mining
   
NetOwlThe most recent week's enteropathogen related abstracts from PubMed® are available here, analyzed by ERIC-NetOwl to extract relevant facts on bacterial genomics. Latest articles are current as of February 7, 2010. Click here for a full page listing.
Show All Articles
There were no latest articles available for the past 7 days. Data displayed below is the latest for the last 30 days.
1. PMID 20109750: Host-microbial interactions in childhood atopy: Toll-like receptor 4 (TLR4), CD14, and fecal Escherichia coli.
2. PMID 20110508: Direct restart of a replication fork stalled by a head-on RNA polymerase.
3. PMID 20112455: Structure of the Ni(II) complex of Escherichia coli peptide deformylase and suggestions on deformylase activities depending on different metal(II) centres.
4. PMID 20111861: Asymmetric synthesis of (S)-3-chloro-1-phenyl-1-propanol using Saccharomyces cerevisiae reductase with high enantioselectivity.
5. PMID 20111865: Plasmid Encoded AcrAB-TolC Tripartite Multidrug-Efflux System in Acidiphilium symbioticum H8.
Returned 163 Articles    Page: 
Data Summaries
   




Annotation Summary
 
Genes CDS rRNA tRNA misc_RNA pseudogenes EC # GO ID IS Elements Unique PubMed ID
Total 839,255 811,693 3,009 13,530 3,882 7,141 211,369 543,283 7,164 8,484
Changed 803,883 785,334 1,878 8,485 1,537 6,649 210,680 545,008 7,164 8,484


Genome Summary
 
Class of Organism Complete Draft Total
Escherichia 21 21 42
Salmonella 17 12 29
Shigella 9 1 10
Yersinia 12 17 29
Other Genomes 11 0 11
Totals: 70 51 121

Search All Genomes
  

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 (example: yopH)

Advanced Search
Tools
  

Annotations
Displays comprehensive annotations, history, sequence, external DB links, etc.
   Query Intersection    Perlegen SNP Data    Virulence Genes in ERIC    Guide to Annotation    ERIC Annotation SOPs

BLAST
Displays results of protein or nucleotide BLAST for query sequence.

Graphical Genome Browser
Displays query location and content on respective genome(s).

Microarray Analysis:
An integrated set of web-based analysis tools and a data management system for storing and analyzing gene expression data.
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   Guide to mAdb
   Affymetrix Upload

Mauve
Rapid alignment of multiple whole genomes.

Text Mining
Uses text mining technology to retrieve user-selected PubMed abstracts and to display functional relationships for genes and other biological molecules.

Download EnteroFam HMMs and Alignments
EnteroFams are orthologous families of proteins across the enterobacterial genomes.

Latest Genome Additions
  

ERIC Genomes