@article {Wang036053, author = {Zhong Wang and Andre L. Martins and Charles G. Danko}, title = {RTFBSDB: an integrated framework for transcription factor binding site analysis}, elocation-id = {036053}, year = {2016}, doi = {10.1101/036053}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Transcription factors (TFs) regulate complex programs of gene transcription by binding to short DNA sequence motifs. Here we introduce rtfbsdb, a unified framework that integrates a database of more than 65,000 TF binding motifs with tools to easily and efficiently scan target genome sequences. Rtfbsdb clusters motifs with similar DNA sequence specificities and optionally integrates RNA-seq or PRO-seq data to restrict analyses to motifs recognized by TFs expressed in the cell type of interest. Our package allows common analyses to be performed rapidly in an integrated environment.Availability: rtfbsdb is available via github (https://github.com/Danko-Lab/rtfbsdb).}, URL = {https://www.biorxiv.org/content/early/2016/01/05/036053}, eprint = {https://www.biorxiv.org/content/early/2016/01/05/036053.full.pdf}, journal = {bioRxiv} }