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Welcome to '''[[Tregwiki:Max]]'s Wiki on Transcriptional Regulation'''. ([[Tregwiki:max|who's max?]])
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Welcome to '''[[Tregwiki:Max]]'s Wiki on Transcriptional Regulation'''. ([[Tregwiki:Max|who's max?]])
''"Man is a tool-using Animal. Nowhere do you find him without tools; without tools he is nothing, with tools he is all." (Thomas Carlyle)''
''"Man is a tool-using Animal. Nowhere do you find him without tools; without tools he is nothing, with tools he is all." (Thomas Carlyle)''
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** Sort by Function: [[Tregwiki:Gene Ontology Tools]]
** Sort by Function: [[Tregwiki:Gene Ontology Tools]]
** Download: [[Tregwiki:Downloading promotors]] aka upstream regions ''en masse''
** Download: [[Tregwiki:Downloading promotors]] aka upstream regions ''en masse''
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** Align: [[Tregwiki:Aligning promotors|Align non-coding sequences]] or use [[Tregwiki:Whole-Genome Alignments]] to [[FindConservedNoncoding|delineate conserved non-coding]] elements
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** Align: [[Tregwiki:Aligning promotors|Align non-coding sequences]] or use [[Tregwiki:Whole-Genome Alignments]] to [[Tregwiki:FindConservedNoncoding|delineate conserved non-coding]] elements
** Visualize [[Tregwiki:Multi-sequence visualization of features]]
** Visualize [[Tregwiki:Multi-sequence visualization of features]]
** Altogether: [[Tregwiki:Enhancerprediction|Prediction of clusters of sites]] with optional conservation
** Altogether: [[Tregwiki:Enhancerprediction|Prediction of clusters of sites]] with optional conservation
*Binding sites:
*Binding sites:
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** Look up: In databases of known [[Tregwiki:collected regulatory elements]]
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** Look up: In databases of known [[Tregwiki:Collected regulatory elements]]
** Scan: [[Tregwiki:Scanning promotors]] or enhancers for binding site matrices or consensus sequences
** Scan: [[Tregwiki:Scanning promotors]] or enhancers for binding site matrices or consensus sequences
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** Predict: [Tregwiki:http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[calculate statistics]] of DNA-words or [[Tregwiki:discover motif combinations]]
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** Predict: [http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[Tregwiki:Calculate statistics]] of DNA-words or [[Tregwiki:Discover motif combinations]]
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* [[Tregwiki:recent bibliography|Recent papers on regulation]]
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* [[Tregwiki:Recent bibliography|Recent papers on regulation]]
*Transcription Factors: (new)
*Transcription Factors: (new)
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* General topics link collection:
* General topics link collection:
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** [[Libraries for Programmers]] working on transcriptional regulation
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** [[Tregwiki:Libraries for Programmers]] working on transcriptional regulation
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** [[People working on transcription regulation]] (please add yourself here!)
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** [[Tregwiki:People working on transcription regulation]] (please add yourself here!)
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** [[General websites]] for transcriptional regulation
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** [[Tregwiki:General websites]] for transcriptional regulation
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** [[The structure of DNA]] is a topic where I'm clueless. I'm merely collecting any kind of links here.
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** [[Tregwiki:The structure of DNA]] is a topic where I'm clueless. I'm merely collecting any kind of links here.
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** [[In-situ databases]]
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** [[Tregwiki:In-situ databases]]
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** [[Conferences]]
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** [[Tregwiki:Conferences]]
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** The [[Jim Kent Source Tree]]
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** The [[Tregwiki:Jim Kent Source Tree]]
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There are a couple of [[similar link collections]] on the web.
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There are a couple of [[Tregwiki:Similar link collections]] on the web.
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Sometimes [[Gene Ontology related]] tools are useful when working with transcriptional regulation.
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Sometimes [[Tregwiki:Gene Ontology related]] tools are useful when working with transcriptional regulation.

Revision as of 14:58, 11 December 2007

Welcome to Tregwiki:Max's Wiki on Transcriptional Regulation. (who's max?)

"Man is a tool-using Animal. Nowhere do you find him without tools; without tools he is nothing, with tools he is all." (Thomas Carlyle)

I am collecting links related to bioinformatics and binding site prediction (Tregwiki:Why is this a difficult problem?). There are usually many different solutions for every problem in bioinformatics. This list might shorten your mileage when choosing an appropriate one.


There are a couple of Tregwiki:Similar link collections on the web. Sometimes Tregwiki:Gene Ontology related tools are useful when working with transcriptional regulation.

Personal tools