AlignACE: Difference between revisions
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=About {{PAGENAME}}= | ==About {{PAGENAME}}== | ||
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. | 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. | ||
=Content= | ==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 <ref>PMID:3045325</ref><ref>PMID:3612791</ref> | 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}}= | ==Using {{PAGENAME}}== | ||
==Browsing== | ===Browsing=== | ||
==Searching== | ===Searching=== | ||
==Usage examples== | ===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== | ||
[[RegulonDB]] | *[[RegulonDB]] | ||
=Technology= | ==Technology== | ||
==Web Services/API== | ===Web Services/API==+ | ||
=Discussion= | ==Discussion== | ||
=References= | ==References== | ||
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=External Links= | ==External Links== | ||
[http://arep.med.harvard.edu/ecoli_matrices {{PAGENAME}}] | [http://arep.med.harvard.edu/ecoli_matrices {{PAGENAME}}] | ||
==Discussion of {{PAGENAME}} on other websites== | ==Discussion of {{PAGENAME}} on other websites== | ||
Revision as of 10:12, 27 January 2009
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| Link/URL: |
Abigail Manson McGuire Genetics Dept. Harvard Medical School |
|---|---|
| What: | |
| Who: | |
| Updates: |
in 1998? |
| Upcoming events: |
none |
| Web Services: |
|
| edit table |
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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