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[[Category:Databases]] | |||
[[Category:E. coli Databases]] | |||
[[Category:DNA-binding site Databases]] | |||
[[Category:Bioinformatics Tools]] | |||
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{| {{Prettytable}} width='30%' align="right" id="N46afcc24a73c4" class=" tableEdit Database_table" | |||
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!align=left {{table heading style}} |Link/URL: | |||
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[http://arep.med.harvard.edu/ecoli_matrices AlignACE] | |||
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!align=left {{table heading style}} |What: | |||
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Matrices which search for additional binding sites in the E. coli genomic sequence. | |||
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| | !align=left {{table heading style}} |Who: | ||
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Abigail Manson McGuire | |||
Genetics Dept. | |||
Harvard Medical School | |||
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| Updates | !align=left {{table heading style}} |Updates: | ||
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<i>Last Updated: Nov. 1998</i> | |||
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| Upcoming events | !align=left {{table heading style}} |Upcoming events: | ||
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| Web Services | !align=left {{table heading style}} |Web Services: | ||
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=About {{PAGENAME}}= | <!--box uid=63ce1649aab8b3180235b0af7618f667.1636.N46afcc24a73c4--></protect> | ||
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=Content= | ==About {{PAGENAME}}== | ||
=Using {{PAGENAME}}= | [[Image:Alignace_home.jpg|right|thumb|300px|Home Page]] | ||
==Browsing== | The [http://arep.med.harvard.edu/ecoli_matrices {{PAGENAME}}] website has a collection of predicted transcription factor binding sites based on running [[scanACE]], an algorithm published<ref>PMID:9813115</ref> by the Church lab against the MG1655 genome. | ||
==Searching== | ==Content== | ||
==Usage examples== | AlignACE has a table with links from the 59 DNA-binding proteins for which they have predicted binding sites by extrapolation from footprinting data. There are also summary tables and the code for scanACE and alignACE can be downloaded via a link to a Church lab website. These programs implement the approach of Berg and von Hippel <ref>PMID:3045325</ref><ref>PMID:3612791</ref> | ||
==Using {{PAGENAME}}== | |||
===Browsing=== | |||
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===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= | *[[RegulonDB]] | ||
==Web Services/API== | ==Technology== | ||
=Discussion= | ===Web Services/API=== | ||
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=External Links= | [http://arep.med.harvard.edu/ecoli_matrices {{PAGENAME}}] | ||
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==Discussion of {{PAGENAME}} on other websites== | ==Discussion of {{PAGENAME}} on other websites== | ||
Latest revision as of 00:11, 23 May 2010
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| Link/URL: | |
|---|---|
| What: |
Matrices which search for additional binding sites in the E. coli genomic sequence. |
| Who: |
Abigail Manson McGuire Genetics Dept. Harvard Medical School |
| Updates: |
Last Updated: Nov. 1998 |
| Upcoming events: | |
| Web Services: |
|
| edit table |
See Help:Database_table for how to add or edit information in this section of EcoliWiki.
About AlignACE
The AlignACE website has a collection of predicted transcription factor binding sites based on running scanACE, an algorithm published[1] by the Church lab against the MG1655 genome.
Content
AlignACE has a table with links from the 59 DNA-binding proteins for which they have predicted binding sites by extrapolation from footprinting data. There are also summary tables and the code for scanACE and alignACE can be downloaded via a link to a Church lab website. These programs implement the approach of Berg and von Hippel [2][3]
Using AlignACE
Browsing
Searching
Usage examples
Add links to additional pages describing success stories here.
Technology
Web Services/API
Discussion
References
See Help:References for how to manage references in EcoliWiki.
- ↑ Robison, K et al. (1998) A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol. 284 241-54 PubMed
- ↑ Berg, OG & von Hippel, PH (1988) Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites. J Mol Biol 200 709-23 PubMed
- ↑ Berg, OG & von Hippel, PH (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol. 193 723-50 PubMed