HEARTBEAT

HEARTBEAT (Heidelberg Artificial Transcription Factor Binding Site Engineering and Assembly Tool) is a set of interconnected models and bioinformatic tools which can be used to design and evaluate functional mammalian promoter sequences. HEARTBEAT is self-iterating, with the output always being used to improve the processing of future inputs. HEARTBEAT consists of a dabase which stores the spatial distribution of transcription factor binding sites along human promoters, and co-occurence patterns of transcription factors. We created HEARTBEAT DB by scanning over 4000 promoter sequences from the human genome. The output derived from HEARTBEAT DB provides an initial framework of promoter structure. A HEARTBEAT GUI, (documentation) helps users with the standardized design of promoter sequences. The final piece in the HEARTBEAT portfolio is Fuzzy Logic Network Modeling which analyzes data from natural or random-synthetic promoters to make statements about the structure of an ideal promoter. In the future, experimental results from sequences generated by HEARTBEAT will always fill in and improve the Fuzzy Logic Model which can then be used to improve the software HEARTBEAT GUI is based upon. Thereby, we create a cycle of iterations which will propel HEARTBEAT to become the major resource for synthetic promoter design.