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University of Louisville Bioinformatics

Bioinformatics Research at the University of Louisville


Project:

RBF-TSS: Identification of transcription start site in human using radial basis functions network and oligonucleotide positional frequencies


Authors:

Rami N. Mahdi(1,2) Eric C. Rouchka(1,2)

  1. University of Louisville Department of Computer Engineering and Computer Science.
  2. University of Louisville Department of Bioinformatics Research Group.
Motivation:
RBF-TSS is a novel identification method for identifying transcription start sites that improves upon published TSS detection models. RBF-TSS incorporates a metric feature based on oligonucleotide positional frequencies, taking into account the nature of promoters. A radial basis function network for identifying transcription start sites is created using non-overlapping chunks (windows) of size 50 and 500 on the human genome.

An Adobe PDF slideshow illustrating the features of RBF-TSS is also available: RBF-TSS.pdf



 
Results:
RBF-TSS is freely available as a Java JAR file.

Instructions for using RBF-TSS

VERSION 1.0

  • Download RBF-TSS (zip file) (Updated 10/29/2010) (RBF-TSS.zip)

Training and validation data have been used from the Accurate Recognition of Transcription Starts (ARTS) in Human website (ARTS website).

When using the training and validation data, please cite: Sonnenburg S, Zien A, Ratsch G. (2006) ARTS: Accurate Recognition of Transcription Starts in Human. Bioinformatics, 22(14):e472-e480.

Citation:
Please Cite:

Mahdi RN, Rouchka EC. (2009) RBF-TSS: Identification of transcription start site in human using radial basis functions network and oligonucleotide positional freqeuncies. PLoS One, 4(3):e4878. (10.1371/journal.pone.0004878)


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