Tregwiki:Main Page: Difference between revisions
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Welcome to '''[[Tregwiki:Max]]'s Wiki on Transcriptional Regulation'''. ([[Tregwiki: | 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'' | ||
** Align: [[Tregwiki:Aligning promotors|Align non-coding sequences]] or use [[Tregwiki: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 [[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: | ||
** Look up: In databases of known [[Tregwiki: | ** 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 | ||
** Predict: [ | ** Predict: [http://www.stud.uni-potsdam.de/~haussler/master Discover motifs], [[Tregwiki:Calculate statistics]] of DNA-words or [[Tregwiki:Discover motif combinations]] | ||
* [[Tregwiki: | * [[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: | ||
** [[Libraries for Programmers]] working on transcriptional regulation | ** [[Tregwiki:Libraries for Programmers]] working on transcriptional regulation | ||
** [[People working on transcription regulation]] (please add yourself here!) | ** [[Tregwiki:People working on transcription regulation]] (please add yourself here!) | ||
** [[General websites]] for transcriptional regulation | ** [[Tregwiki: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]] is a topic where I'm clueless. I'm merely collecting any kind of links here. | ||
** [[In-situ databases]] | ** [[Tregwiki:In-situ databases]] | ||
** [[Conferences]] | ** [[Tregwiki:Conferences]] | ||
** The [[Jim Kent Source Tree]] | ** The [[Tregwiki:Jim Kent Source Tree]] | ||
There are a couple of [[ | There are a couple of [[Tregwiki:Similar link collections]] on the web. | ||
Sometimes [[Gene Ontology related]] tools are useful when working with transcriptional regulation. | Sometimes [[Tregwiki:Gene Ontology related]] tools are useful when working with transcriptional regulation. | ||
Revision as of 12:58, 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.
- 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: Discover motifs, Tregwiki: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:
- Tregwiki:Libraries for Programmers working on transcriptional regulation
- Tregwiki:People working on transcription regulation (please add yourself here!)
- Tregwiki:General websites for transcriptional regulation
- Tregwiki:The structure of DNA is a topic where I'm clueless. I'm merely collecting any kind of links here.
- Tregwiki:In-situ databases
- Tregwiki:Conferences
- The Tregwiki:Jim Kent Source Tree
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.
