What’s the Answer? (promoter identification)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question was one I saw some time back, but I found the list of tools in the top rated answer handy:

Identification of promoters from gene sequences and a vertebrate genome assembly

I have a number of genes which I’d like to locate in a whole-genome assembly, in order to identify the genes’ promoters. In the past I’ve done this manually using BLAST and BLAT, which has worked well, but the process is quite time-intensive (because I have to take into account introns and exons). Now I find myself in a situation where I need to find the promoters for 100s of genes.

Is there a pipeline or tool which will, given gene sequences and allowing for introns, allow me to identify automate the detection of gene promoters? I’d rather not reinvent the wheel.

David M

As one of the answers indicated, we are fans of MEME  suite tools, but there are a range of things that might be suitable depending on your species starting point and your goals. MDscan is another tool to explore.  Check out the top-rated answer for the list.