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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 |
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* 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] |
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| - | + | 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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Current revision
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.
