Tregwiki:Main Page
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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 [[[Tregwiki:Discover motif combinations|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.
