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{{Pagetop}}
[[Category:Databases]]
[[Category:E. coli Databases]]
[[Category:IECA Portal]]
<protect><!--box uid=63ce1649aab8b3180235b0af7618f667.1714.Y4864976062ca6-->
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
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{| {{Prettytable}} width='30%' align="right"  id="Y4864976062ca6"  class=" tableEdit Database_table" 


'''PEC'''
'''You can help [[EcoliWiki]] by editing the content of this page.  For information about obtaining editing privileges, see [[E._coli_Wiki:Membership]]''' 
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
|  colspan = '2' | '''{{PAGENAME}}'''
|-
|-
| width='30%' | Who:
!align=left {{table heading style}} |Link/URL:
| ''proprietor''
||
[http://www.shigen.nig.ac.jp/ecoli/pec/ http://www.shigen.nig.ac.jp/ecoli/pec/]
|-
|-
| width='30%' | What:
!align=left {{table heading style}} |What:
| ''short description''
||
Profiling ''E. coli'' Chromosome
 
PEC focuses on gene function
|-
|-
| Where:
!align=left {{table heading style}} |Who:
| [http://www.shigen.nig.ac.jp/ecoli/pec/  {{PAGENAME}}]
||
National Institute of Genetics (Japan)
|-
|-
| Updates
!align=left {{table heading style}} |Updates:
|
||
 
|-
|-
| Upcoming events
!align=left {{table heading style}} |Upcoming events:
| ''link to event calendar, if applicable''
||
 
|-
|-
| Web Services
!align=left {{table heading style}} |Web Services:
|
||
 
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.1714.Y4864976062ca6&page=1714&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table]</span> ||
|}
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=About {{PAGENAME}}=
<!--box uid=63ce1649aab8b3180235b0af7618f667.1714.Y4864976062ca6--></protect>
''Add general information here''  
 
[http://www.shigen.nig.ac.jp/ecoli/pec/ {{PAGENAME}}] is...
 
=Content=
==About {{PAGENAME}}==
=Using {{PAGENAME}}=
PEC is a curated resource that gives general information about the genes in MG1655<ref name='PMID:18392982'/>. 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.
==Browsing==
 
==Searching==
==Content==
==Usage examples==
Essential Genes & Minimal Genome <BR>
Genes<BR>
Deletions <BR>
 
Comparative Genomics <BR>
BLAST<BR>
Tools<BR>
Strains<BR>
Contigs<BR>
 
==Using {{PAGENAME}}==
===Browsing===
[[Image:PEC genome browser.jpg|Figure 1. The PEC genome browser|thumb|500px]]
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.
 
<br clear='all'/>
 
===Searching===
==== for gene names ====
[[Image:pec search.jpg|Figure 2. Results of a search for "lac" using the Genes option|thumb|500px]]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 "ga'''lac'''tose, "'''lac'''tamase", or "aceto'''lac'''tate".  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<ref name='PMID:15612923'/><ref name='PMID:17700540'/>
 
===Usage examples===
''Add links to additional pages describing success stories here.''
''Add links to additional pages describing success stories here.''


=Other sites with related content=
==Other sites with related content==
=Technology=
==Technology==
==Web Services/API==
===Downloads===
=Discussion=
[http://www.shigen.nig.ac.jp/ecoli/pec/download.jsp downloadable files] include:
==Trackbacks==
* ''E. coli'' maps based on the PEC genome browser as pdf files
[[Trackbacks|''What are trackbacks?'']]  ''This feature is not yet functional''
* PEC data as tab-delimited text.
===Web Services/API===
 
==Discussion==
 
==References==
{{BacktoTop}}
{{RefHelp}}
<references />


=References=
==External Links==
=External Links=
[http://www.shigen.nig.ac.jp/ecoli/pec/  {{PAGENAME}}]
[http://www.shigen.nig.ac.jp/ecoli/pec/  {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==
==Discussion of {{PAGENAME}} on other websites==

Latest revision as of 00:11, 23 May 2010

You can help EcoliWiki by editing the content of this page. For information about becoming a registered user and obtaining editing privileges, see Help:Accounts.

Link/URL:

http://www.shigen.nig.ac.jp/ecoli/pec/

What:

Profiling E. coli Chromosome

PEC focuses on gene function

Who:

National Institute of Genetics (Japan)

Updates:
Upcoming events:
Web Services:


edit table


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

Figure 1. The PEC genome browser

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

Figure 2. Results of a search for "lac" using the Genes option

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.

Other sites with related content

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

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. ↑ Yamazaki, Y et al. (2008) Profiling of Escherichia coli Chromosome database. Methods Mol. Biol. 416 385-9 PubMed
  2. ↑ 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
  3. ↑ Kato, J & Hashimoto, M (2007) Construction of consecutive deletions of the Escherichia coli chromosome. Mol. Syst. Biol. 3 132 PubMed

External Links

PEC

Discussion of PEC on other websites

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=PEC&oldid=1094766"