Fly Promoter Libraries
This set of 3 libraries was designed to add state-of-the-art promoter analysis to the repertoire of GenePalette's utility. Searching with the libraries can tell you whether a predicted transcription start site is believable, and suggest the makeup of core promoter elements.
The core promoter is composed of several elements found at specific positions relative to the start of transcription [click here for a review]. For instance, the TATA box is usually ~25-30bp upstream of the transcription start site. The Initator element marks the start of transcription, and there are elements downstream of the Initiator called the DPE (Downstream Promoter Element) and the newly identified MTE (Motif Ten Element [Click for abstract]). These different elements each have a simple consensus, a search of which will yield a surplus of matches in almost any sequence. However, when the elements are combined, and constrained by our knowledge of the spacing between them, searches will be much more specific. Thus, we have created feature libraries which contain all possible combinations of these promoter elements with proper spacing (e.g.: TATA+INR or INR+DPE).
Fly Promoter Library (FlyProm.lib)
Fly Promoter Mismatch Library (FlyPromMM.lib)
Core Promoter Elements Library (CorePromElem.lib)
Library Documentation (FlyPromLibInfo.pdf)
Thanks to Thomas Boulay (Kadonaga Lab) for helping us make these libraries! Questions about the promoter libraries can be directed to mrebeiz@ucsd.edu
Restriction Library
This is the standard restriction library that is packaged with GenePalette. It was taken from a list of NEB restriction enzymes. WARNING: The restriction sites in this library do not look for overlapping CpG, dam or dcm methylation sites.
Restriction Library (RE.lib)