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RTFBSDB: an integrated framework for transcription factor binding site analysis

Zhong Wang, Andre L. Martins, Charles G. Danko
doi: https://doi.org/10.1101/036053
Zhong Wang
1Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY.
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Andre L. Martins
1Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY.
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Charles G. Danko
1Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY.
2Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY.
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  • For correspondence: dankoc@gmail.com
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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).

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted January 06, 2016.
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RTFBSDB: an integrated framework for transcription factor binding site analysis
Zhong Wang, Andre L. Martins, Charles G. Danko
bioRxiv 036053; doi: https://doi.org/10.1101/036053
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RTFBSDB: an integrated framework for transcription factor binding site analysis
Zhong Wang, Andre L. Martins, Charles G. Danko
bioRxiv 036053; doi: https://doi.org/10.1101/036053

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