Piecewise-linear machine-learning model for motif-based prediction of transcription factor binding sites
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
code
LICENSE
README.md

README.md

pltfbsmotif

Piecewise-linear machine-learning model for motif-based prediction of transcription factor binding sites

This repository contains the MATLAB code for a piecewise-linear, data-fusion model for motif-based prediction of transcription factor binding sites. The code was used in the analysis published in the 2010 article Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites (Ramsey et al., Bioinform., 2010).

The MATLAB code in this project was written by Stephen Ramsey (@saramsey) except for six contributed modules:

  • PSWM_MotifLocator.m, BM_Scan.m, basepairs2num.m, readfastaseqs.m: Harri Lähdesmäki (personal communication)
  • readbar.m, writebar.m: Matti Nykter (personal communication)

The contributions of Dr. Lähdesmäki and Dr. Nykter to this project are gratefully acknowledged.

Requirements