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Welcome to '''[[Max]]'s Wiki on Transcriptional Regulation'''. ([[max|who's max?]]) | 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)'' | ||
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]]?). | ||
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]] | ||
** 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]] | ||
** Find Orthologs: [[Finding interspecies-orthologs]] for multiple alignments | ** Find Orthologs: [[Tregwiki:Finding interspecies-orthologs]] for multiple alignments | ||
** Sort by Function: [[Gene Ontology Tools]] | ** Sort by Function: [[Tregwiki:Gene Ontology Tools]] | ||
** Download: [[Downloading promotors]] aka upstream regions ''en masse'' | ** Download: [[Tregwiki: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]] to [[FindConservedNoncoding|delineate conserved non-coding]] elements | ||
** Visualize [[Multi-sequence visualization of features]] | ** Visualize [[Tregwiki: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 [[collected regulatory elements]] | ** Look up: In databases of known [[Tregwiki:collected regulatory elements]] | ||
** Scan: [[Scanning promotors]] or enhancers for binding site matrices or consensus sequences | ** Scan: [[Tregwiki:Scanning promotors]] or enhancers for binding site matrices or consensus sequences | ||
** Predict: [http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[calculate statistics]] of DNA-words or [[discover motif combinations]] | ** Predict: [Tregwiki:http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[calculate statistics]] of DNA-words or [[Tregwiki:discover motif combinations]] | ||
* [[recent bibliography|Recent papers on regulation]] | * [[Tregwiki:recent bibliography|Recent papers on regulation]] | ||
*Transcription Factors: (new) | *Transcription Factors: (new) | ||
** [[Lists of Factors]] by similarity | ** [[Tregwiki:Lists of Factors]] by similarity | ||
* [[Meta-Websites]] that integrate promotor download, motif matching/discovery | * [[Tregwiki:Meta-Websites]] that integrate promotor download, motif matching/discovery | ||
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Revision as of 12:49, 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.
- Promotors/Enhancers/Regulatory Regions:
- Assemble: Tregwiki:Assembling promotors from trace databases
- Narrow down: Predict promotors/enhancers in silico
- Check if ncRNA: Tregwiki:Folding Alignments
- Find Orthologs: Tregwiki:Finding interspecies-orthologs for multiple alignments
- Sort by Function: Tregwiki:Gene Ontology Tools
- Download: Tregwiki:Downloading promotors aka upstream regions en masse
- Align: Align non-coding sequences or use Tregwiki:Whole-Genome Alignments to delineate conserved non-coding elements
- Visualize Tregwiki:Multi-sequence visualization of features
- Altogether: Prediction of clusters of sites with optional conservation
- Binding sites:
- Look up: In databases of known Tregwiki:collected regulatory elements
- Scan: Tregwiki:Scanning promotors or enhancers for binding site matrices or consensus sequences
- Predict: [Tregwiki:http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], calculate statistics of DNA-words or Tregwiki:discover motif combinations
- Transcription Factors: (new)
- Tregwiki:Lists of Factors by similarity
- Tregwiki: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.
