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Crf-based Tfbs Finding system CTF

Predicts transcription factor binding sties (TFBSs). CTF is based on Conditional Random Fields (CRFs) and can capture sophisticated dependency and integrate information from different sources. The software can be a useful complement to ChIP-seq and other experimental methods for TFBS identification. It was evaluated on 13 TFBS datasets with three types of features,(i) the Position Weight Matrix(PWM), (ii) the distance to Transcription start sites (TSS proximity), and (iii) histone markers.

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CTF classification

CTF specifications

Software type:
Package/Module
Restrictions to use:
Academic or non-commercial use
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Operating system:
Unix/Linux
Version:
0.91
Maintained:
Yes

CTF distribution

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CTF support

Maintainer

  • Chaochun Wei <>

Credits

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Publications

Institution(s)

School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Bioinformation Technology, Shanghai, China; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA

Funding source(s)

Supported by grants from the National Natural Science Foundation of China (60970050, 31100957), the Shanghai Pujiang Program (09PJ1407900), K.C. Wong Education Foundation, Hong Kong and China Postdoctoral Science Foundation fund (20110490758).

Link to literature

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