Jun 132016
 

TFBS Scanner

:: DESCRIPTION

TFBS Scanner provides command line software toolsets for two useful types of TFBS (Transcription Factor Binding Site) Scanning using Positional Weight Matrices (PWMs):

The Scanner Toolset
Scanning with a fixed background model (can be toggled to 0th order or 1st order Markov, currently set as 1st order), with PWM-specific thresholds generated using this same background

The SpeakerScan Toolset
Scanning with a local background correction, outputs log-likelihood scores which can then be post-processed as desired

::DEVELOPER

Megraw Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

  TFBS Scanner

:: MORE INFORMATION

Citation

Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M. (2014).
Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.
Plant Cell, 26:2746-60.

Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG. (2009).
A transcription factor affinity based code for mammalian transcription initiation.
Genome Research, 19:644-56.

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