PEC
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| What: |
Profiling E. coli Chromosome PEC focuses on gene function |
| Who: |
National Institute of Genetics (Japan) |
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| Web Services: |
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| edit table |
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Contents
About PEC
PEC is a curated resource that gives general information about the genes in MG1655[1]. The main focus of PEC is to assist in discovering the functions of gene with unknown function. Another main focus of PEC is to represent the advances towards finding the minimal genome.
Content
Essential Genes & Minimal Genome
Genes
Deletions
Comparative Genomics
BLAST
Tools
Strains
Contigs
Using PEC
Browsing
PEC provides circular and linear genome views. The linear view is a genome browser. Figure 1 shows an area of the genome. The upper panel includes navigation controls and a thumbnail to show what part of the circular genome is displayed. The W and M buttons toggle the view between the MG1655 and W3110 genomes. Below the control panel, a series of genome sections are displayed. The grey bar at the top of each panel provides coordinates. Below that, dashed lines indicate the positions of Kohara clones in the region. The genes are indicated by glyphs, where nonessential genes are shown in green and essential genes are shown in red. The last set of lines show the positions of deletions. The black part of the line shows the extent of the deletion while the yellow portion, if present, shows the extent of DNA in a complementing plasmid that was used to provide essential genes in strains containing the deletion.
Searching
for gene names
PEC includes a quick search box at the top of every page. Type in the gene name and choose whether to search all fields, genes/RNA, or deletions. PEC searches are automatically wildcard queries; searching for "lac" finds anything with the substring "lac", such as "galactose, "lactamase", or "acetolactate". Thus, when searching for genes, it is best to select genes/RNA from the pulldown menu. Figure 2 shows the results of a search for "lac". Note that PEC finds lac in the gene symbol or in the alternative name. This means that you can also search using b numbers. PEC does not (as of Aug 2008) contain ECK or JW numbers.
Clicking on Genes from the navigation menu provides a more advanced gene search, with options to search by
- gene name
- genomic position
- GO terms
- essential/nonessential/unknown
for gene families
PEC provides a search for genes/products based on motif types.
for deletions
PEC provides a search for information about deletions, including large collections of engineered deletions from a minimal genome project[2][3]
Usage examples
Add links to additional pages describing success stories here.
Technology
Downloads
downloadable files include:
- E. coli maps based on the PEC genome browser as pdf files
- PEC data as tab-delimited text.
Web Services/API
Discussion
References
See Help:References for how to manage references in EcoliWiki.
- ↑ Yamazaki, Y et al. (2008) Profiling of Escherichia coli Chromosome database. Methods Mol. Biol. 416 385-9 PubMed
- ↑ Hashimoto, M et al. (2005) Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol. Microbiol. 55 137-49 PubMed
- ↑ Kato, J & Hashimoto, M (2007) Construction of consecutive deletions of the Escherichia coli chromosome. Mol. Syst. Biol. 3 132 PubMed
