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.

New Text Mining Word Cloud Feature
The Literature Text Mining Tool has been upgraded to allow visualization of the Search Extraction results in a "tag cloud" representation, where increased frequency of occurrence of a term in the results will have a larger font size for that term in the tag cloud. The view can be toggled with the "View Entity Cloud" button to see just gene, gene product, or operon names - and then toggled back with the "View Word Cloud" button. Clicking a word in the cloud adds that term to the current search and recomputes the cloud.

Download EnteroFam HMMs and Alignments
EnteroFams are orthologous families of proteins across the enterobacterial genomes. Each EnteroFam is based on a seed alignment of orthologous proteins from eight genomes and converted to a HMM. These HMMs, alignments, and human readable output are now available for download. EnteroFam annotations are available in the ASAP database.

The Pathogen Functional Genomics Resource Center announces a program to obtain the Affymetrix E. coli FDA-ECSG microarray
The NIAID sponsored PFGRC contract at the JCVI, in collaboration with the FDA and Affymetrix is making available, at no cost to investigators, the Affymetrix FDA-ECSG E. coli microarray. This microarray contains 23,090 probe set targets representing 32 diverse E. coli and Shigella strains as well as 46 related plasmid sequences. The microarrays are designed based on 11 oligo pairs per gene target. The arrays do not target the complete genome, and thus cannot be used for direct resequencing.

Individuals are invited to submit their requests through the PFGRC microarray application process. A clear and well thought out project proposal to which these microarrays will be applied is essential and collaboration with the PFGRC is encouraged in these proposals.

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.
   Login
   Account Request
   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.

ERIC Genomes

• Escherichia fergusonii ATCC 35469
• Shigella flexneri 2457T
• Yersinia pestis India 195
• Yersinia pestis Nepal516A
• Yersinia pestis PEXU2