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
 * 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


 * 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.