Hi!
Im doing a bioinformatics exercise, but Im new to this and now I need help.. I have a list of 5 genes that Im going to analyze with different bioinformatic tools. They are all transcription factors, and I want to "prove" that they are part of the immediate early response process. As a part of doing that, I want to identify TATA boxes in their promoter regions, but the problem is I dont know how to do this. Is there any way to find TATA boxes with some of the following tools; Meme Suite, UCSC genome browser, Ensembl, Jaspar, Transfac, or Genomic Hyperbrowser? And how do I find them (if it is possible)?
Thanks in advance!
You can use http://homer.salk.edu/homer/motif/ or http://homer.salk.edu/homer/motif/fasta.html THE TATA box position-weight matrix can be found in the JASPAR database and you can use it for scanning the sequences.