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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|Msx'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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I am collecting links related to bioinformatics and binding site prediction ([[Tregwiki:Why is this a difficult problem]]?).
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I am collecting links related to bioinformatics and binding site prediction ([[Tregwiki:Why is this a difficult problem|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 usually many different solutions for every problem in bioinformatics. This list might shorten your mileage when choosing an appropriate one.
* Promotors/Enhancers/Regulatory Regions:
* Promotors/Enhancers/Regulatory Regions:
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** Assemble: [[Tregwiki:Assembling promotors from trace databases]]
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** Assemble: [[Tregwiki:Assembling promotors from trace databases|Assembling promotors from trace databases]]
** Narrow down: [[Tregwiki:Predict promotor regions|Predict promotors/enhancers]] in silico
** Narrow down: [[Tregwiki:Predict promotor regions|Predict promotors/enhancers]] in silico
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** Check if ncRNA: [[Tregwiki:Folding Alignments]]
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** Check if ncRNA: [[Tregwiki:Folding Alignments|Folding Alignments]]
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** Find Orthologs: [[Tregwiki:Finding interspecies-orthologs]] for multiple alignments
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** Find Orthologs: [[Tregwiki:Finding interspecies-orthologs|Finding interspecies-orthologs]] for multiple alignments
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** Sort by Function: [[Tregwiki:Gene Ontology Tools]]
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** Sort by Function: [[Tregwiki:Gene Ontology Tools|Gene Ontology Tools]]
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** Download: [[Tregwiki:Downloading promotors]] aka upstream regions ''en masse''
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** Download: [[Tregwiki:Downloading promotors|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 [[Tregwiki:FindConservedNoncoding|delineate conserved non-coding]] elements
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** Align: [[Tregwiki:Aligning promotors|Align non-coding sequences]] or use [[Tregwiki:Whole-Genome Alignments|Whole-Genome Alignments]] to [[Tregwiki:FindConservedNoncoding|delineate conserved non-coding]] elements
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** Visualize [[Tregwiki:Multi-sequence visualization of features]]
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** Visualize [[Tregwiki:Multi-sequence visualization of features|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|Collected regulatory elements]]
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** Scan: [[Tregwiki:Scanning promotors]] or enhancers for binding site matrices or consensus sequences
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** Scan: [[Tregwiki:Scanning promotors|Scanning promotors]] or enhancers for binding site matrices or consensus sequences
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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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** Predict: [http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[Tregwiki:Calculate statistics|Calculate statistics]] of DNA-words or [[[Tregwiki:Discover motif combinations|Discover motif combinations]]
* [[Tregwiki:Recent bibliography|Recent papers on regulation]]
* [[Tregwiki:Recent bibliography|Recent papers on regulation]]
*Transcription Factors: (new)
*Transcription Factors: (new)
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** [[Tregwiki:Lists of Factors]] by similarity
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** [[Tregwiki:Lists of Factors|Lists of Factors]] by similarity
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* [[Tregwiki:Meta-Websites]] that integrate promotor download, motif matching/discovery
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* [[Tregwiki:Meta-Websites|Meta-Websites]] that integrate promotor download, motif matching/discovery
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* General topics link collection:
* General topics link collection:
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** [[Tregwiki:Libraries for Programmers]] working on transcriptional regulation
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** [[Tregwiki:Libraries for Programmers|Libraries for Programmers]] working on transcriptional regulation
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** [[Tregwiki:People working on transcription regulation]] (please add yourself here!)
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** [[Tregwiki:People working on transcription regulation|People working on transcription regulation]] (please add yourself here!)
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** [[Tregwiki:General websites]] for transcriptional regulation
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** [[Tregwiki:General websites|General websites]] for transcriptional regulation
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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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** [[Tregwiki:The structure of DNA|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:In-situ databases]]
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** [[Tregwiki:In-situ databases|In-situ databases]]
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** [[Tregwiki:Conferences]]
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** [[Tregwiki:Conferences|Conferences]]
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** The [[Tregwiki:Jim Kent Source Tree]]
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** [http://genomewiki.cse.ucsc.edu/index.php/The_source_tree The Jim Kent Source Tree]
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There are a couple of [[Tregwiki:Similar link collections]] on the web.
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There are a couple of [[Tregwiki:Similar link collections|Similar link collections]] on the web.
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Sometimes [[Tregwiki:Gene Ontology related]] tools are useful when working with transcriptional regulation.
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Sometimes [[Tregwiki:Gene Ontology related|Gene Ontology related]] tools are useful when working with transcriptional regulation.

Revision as of 16:07, 11 December 2007

Welcome to Msx'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 (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.

  • Meta-Websites that integrate promotor download, motif matching/discovery

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

Personal tools