Tregwiki:Main Page
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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.
