Tregwiki:Main Page

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
  • 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]]

• Recent papers on regulation

• 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.