title: CTF: a CRF-based transcription factor binding sites finding system.
abstract: BACKGROUND
  Identifying the location of transcription factor bindings is crucial to understand transcriptional regulation. Currently, Chromatin Immunoprecipitation followed with high-throughput Sequencing (ChIP-seq) is able to locate the transcription factor binding sites (TFBSs) accurately in high throughput and it has become the gold-standard method for TFBS finding experimentally. However, due to its high cost, it is impractical to apply the method in a very large scale. Considering the large number of transcription factors, numerous cell types and various conditions, computational methods are still very valuable to accurate TFBS identification.
  
  
  RESULTS
  In this paper, we proposed a novel integrated TFBS prediction system, CTF, based on Conditional Random Fields (CRFs). Integrating information from different sources, CTF was able to capture patterns of TFBSs contained in different features (sequence, chromatin and etc) and predicted the TFBS locations with a high accuracy. We compared CTF with several existing tools as well as the PWM baseline method on a dataset generated by ChIP-seq experiments (TFBSs of 13 transcription factors in mouse genome). Results showed that CTF performed significantly better than existing methods tested.
  
  
  CONCLUSIONS
  CTF is a powerful tool to predict TFBSs by integrating high throughput data and different features. It can be a useful complement to ChIP-seq and other experimental methods for TFBS identification and thus improve our ability to investigate functional elements in post-genomic era.
  
  
  BACKGROUND
  CTF is freely available to academic users at: http://cbb.sjtu.edu.cn/~ccwei/pub/software/CTF/CTF.php.
authors.affiliation: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
authors.forename: Yupeng
authors.initials: Y
authors.lastname: He
authors.forename: Yizhe
authors.initials: Y
authors.lastname: Zhang
authors.forename: Guangyong
authors.initials: G
authors.lastname: Zheng
authors.forename: Chaochun
authors.initials: C
authors.lastname: Wei
mesh_terms: D000465:Algorithms; D000818:Animals; D019540:Area Under Curve; D001665:Binding Sites; D016208:Databases, Factual; D016678:Genome; D020407:Internet; D051379:Mice; D011485:Protein Binding; D012372:ROC Curve; D012984:Software; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors