Logo2PWM is a tool to convert sequence logo back to position weight matrix.

In the field of molecular biology, there are often situations that in a publication, only the sequence logos of the motifs are provided, however, the corresponding PWMs are hard to be acquired. In order to do more researches on these motifs, we need a tool to quickly and accurately convert the sequence logos back to PWMs, that is why we made Logo2PWM.

Folder description

./source_code/ - source code

./server_source_code/ - server source code

Tutorial

Run from source code

Download source code, open MATLAB, go to to the location of f_logo_to_PWM_publish.m (e.g.: ./source_code/):

>> f_logo_to_PWM_publish([logo image file])

or

>> f_logo_to_PWM_publish([logo image file], [#letter columns])

Please refer this article for demos, design and algorithms.

Compile and run executable

Install MATLAB compiler runtime 9.0; in MATLAB, input:

>> mcc -m f_logo_to_PWM_publish.m

The executable will be generated in place.

The sample compiled executables for Windows and OSX locate at ./server_source_code/ with name f_logo_to_PWM_publish.

To run executable, open a terminal/cmd:

$ [executable] [logo image file] [#letter columns (optional)]

Deploy the server

Make sure Python and Flask are installed, then go to ./server_source_code/server/, run:

python ./run.py

A running server

Reference

Please support us by citing this article:

BibTex:

 @article{gao2017logo2pwm,
  title={Logo2PWM: a tool to convert sequence logo to position weight matrix},
  author={Gao, Zhen and Liu, Lu and Ruan, Jianhua},
  journal={BMC genomics},
  volume={18},
  number={6},
  pages={709},
  year={2017},
  publisher={BioMed Central}
 }

Many thanks for your support!