Introduction

Nu-OSCAR (Nucleosome-Occupancy Study for Cis-elments Accurate Recognition) is a program that can be used to identify binding sites of known transcription factors, which further incorporates nucleosome occupancy around sites on promoter regions, thereby improvind the accuracy of predition. The derivation of the the algorithm is based on a biophysical view of interactions between protein factors and nucleosome DNA. For more details about Nu-OSCAR, please see the [manuscript of Nu-oscar] and [Supplementary Tables].

For questions about this web site or if you encounter any problems, do not hesitate to contact Bo Jiang . We are open to any suggestions or remarks concerning this web interface.

 

Input known Binding Sites

You may choose a yeast transcription factor from to search its binding sites on the sequences uploaded below.

If you choose "specified by user" above, you can input your konwn binding sites of a novel transcription factor below in Fasta format (example, format). Average predicted nucleosome occupancy of each binding site (see Methods in our manuscript) could be given if available, and this additional information can aid the recognition of potential binding sites. Note that the width of all input binding sites must be equal (if not, please fill in the gap with 'N') , and be specified in the refline.



Input Promoter Sequences

DNA Sequences (Optional)
DNA Sequences should be submitted in Fasta format (example, format). Nulceosome occupancy predition will be applied, and our program will screen both strands of promoter sequences to identify potential binding sites of the transcription factor. The length of each sequence must be larger than 157 base pairs (for more details about nucleosome occupancy predition, please go to Segal's lab).



Nucleosome Occupancy Predition Model

Select a model to predict nucleosome occpuancy

Parameters

Sensitivity

A parameter v , which is ranging from 0 to 1, is used to control the sensitivity of the classifier The meaning of this parameter can be found in our paper.

Parameter v =