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Welcome to '''[[Max]] | Welcome to '''[[Tregwiki:Max|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)'' | ||
I am collecting links related to bioinformatics and binding site prediction ([[Why is this a difficult problem]]?). | 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: | ||
** Assemble: [[Assembling promotors from trace databases]] | ** Assemble: [[Tregwiki:Assembling promotors from trace databases|Assembling promotors from trace databases]] | ||
** Narrow down: [[Predict promotor regions|Predict promotors/enhancers]] in silico | ** Narrow down: [[Tregwiki:Predict promotor regions|Predict promotors/enhancers]] in silico | ||
** Check if ncRNA: [[Folding Alignments]] | ** Check if ncRNA: [[Tregwiki:Folding Alignments|Folding Alignments]] | ||
** Find Orthologs: [[Finding interspecies-orthologs]] for multiple alignments | ** Find Orthologs: [[Tregwiki:Finding interspecies-orthologs|Finding interspecies-orthologs]] for multiple alignments | ||
** Sort by Function: [[Gene Ontology Tools]] | ** Sort by Function: [[Tregwiki:Gene Ontology Tools|Gene Ontology Tools]] | ||
** Download: [[Downloading promotors]] aka upstream regions ''en masse'' | ** Download: [[Tregwiki:Downloading promotors|Downloading promotors]] aka upstream regions ''en masse'' | ||
** Align: [[Aligning promotors|Align non-coding sequences]] or use [[Whole-Genome Alignments]] to [[FindConservedNoncoding|delineate conserved non-coding]] elements | ** 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 | ||
** Visualize [[Multi-sequence visualization of features]] | ** Visualize [[Tregwiki:Multi-sequence visualization of features|Multi-sequence visualization of features]] | ||
** Altogether: [[Enhancerprediction|Prediction of clusters of sites]] with optional conservation | ** Altogether: [[Tregwiki:Enhancerprediction|Prediction of clusters of sites]] with optional conservation | ||
*Binding sites: | *Binding sites: | ||
** Look up: In databases of known [[ | ** Look up: In databases of known [[Tregwiki:Collected regulatory elements|Collected regulatory elements]] | ||
** Scan: [[Scanning promotors]] or enhancers for binding site matrices or consensus sequences | ** [[Tools for matrices|Visualize and compare your results]] | ||
** Predict: [http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[ | ** Scan: [[Tregwiki:Scanning promotors|Scanning promotors]] or enhancers for binding site matrices or consensus sequences | ||
** 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]] | ||
*Transcription Factors: (new) | *Transcription Factors: (new) | ||
** [[Lists of Factors]] by similarity | ** [[Tregwiki:Lists of Factors|Lists of Factors]] by similarity | ||
* [[Meta-Websites]] that integrate promotor download, motif matching/discovery | * [[Tregwiki:Meta-Websites|Meta-Websites]] that integrate promotor download, motif matching/discovery | ||
---- | ---- | ||
* General topics link collection: | * General topics link collection: | ||
** [[Libraries for Programmers]] working on transcriptional regulation | ** [[Tregwiki:Libraries for Programmers|Libraries for Programmers]] working on transcriptional regulation | ||
** [[People working on transcription regulation]] (please add yourself here!) | ** [[Tregwiki:People working on transcription regulation|People working on transcription regulation]] (please add yourself here!) | ||
** [[General websites]] for transcriptional regulation | ** [[Tregwiki:General websites|General websites]] for transcriptional regulation | ||
** [[The structure of DNA]] is a topic where I'm clueless. I'm merely collecting any kind of links here. | ** [[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. | ||
** [[In-situ databases]] | ** [[Tregwiki:In-situ databases|In-situ databases]] | ||
** [[Conferences]] | ** [[Tregwiki:Conferences|Conferences]] | ||
** The | ** [http://genomewiki.cse.ucsc.edu/index.php/The_source_tree The Jim Kent Source Tree] | ||
There are a couple of [[Tregwiki:Similar link collections|Similar link collections]] on the web. | |||
Sometimes [[Tregwiki:Gene Ontology related|Gene Ontology related]] tools are useful when working with transcriptional regulation. | |||
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Latest revision as of 08:06, 4 March 2008
Welcome to 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 (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.
- Promotors/Enhancers/Regulatory Regions:
- Assemble: Assembling promotors from trace databases
- Narrow down: Predict promotors/enhancers in silico
- Check if ncRNA: Folding Alignments
- Find Orthologs: Finding interspecies-orthologs for multiple alignments
- Sort by Function: Gene Ontology Tools
- Download: Downloading promotors aka upstream regions en masse
- Align: Align non-coding sequences or use Whole-Genome Alignments to delineate conserved non-coding elements
- Visualize Multi-sequence visualization of features
- Altogether: Prediction of clusters of sites with optional conservation
- Binding sites:
- Look up: In databases of known Collected regulatory elements
- Visualize and compare your results
- Scan: Scanning promotors or enhancers for binding site matrices or consensus sequences
- Predict: Discover motifs, Calculate statistics of DNA-words or Discover motif combinations
- Transcription Factors: (new)
- Lists of Factors by similarity
- Meta-Websites that integrate promotor download, motif matching/discovery
- General topics link collection:
- Libraries for Programmers working on transcriptional regulation
- People working on transcription regulation (please add yourself here!)
- General websites for transcriptional regulation
- The structure of DNA is a topic where I'm clueless. I'm merely collecting any kind of links here.
- In-situ databases
- Conferences
- The Jim Kent Source Tree
There are a couple of Similar link collections on the web. Sometimes Gene Ontology related tools are useful when working with transcriptional regulation.
