README.md

In tomateba/p53retriever: detection and display of p53 putative response elements (REs) on DNA sequences

p53retriever

R package to locate and display p53 putative response elements on a DNA sequence

Overview

p53retriever is an R package implementing a pattern search algorithm that maps p53 response elements (REs) and ranks them according to predicted transactivation potentials in five classes. Besides canonical, full site REs, p53retriever contains specific pattern searches for non-canonical half sites and 3/4 sites. REs can be displayed along the input sequence in a graphical layout.

The rules formalized in the model are based on observations obtained during several years of experiments using the yeast-based assays, including the results presented in (Inga et al MCB2002; Tomso et al, PNAS 2005; Jegga et al PNAS 2008; Jordan et al PloS Genetics 2008; Menendez et PNAS 2010).

Reference

Please cite the following article when using p53retriever:

T Tebaldi, S Zaccara, F alessandrini, A Bisio, Y Ciribilli, A Inga. Whole-genome cartography of p53 response elements ranked on transactivation potential. BMC Genomics. 2015 Jun 17;16:464

License

Installation

To install p53retriever, directly from github:

install.packages("devtools")
library("devtools")
install_github("tomateba/p53retriever")

Usage

This code shows how p53retriever can be used on the promoter sequence of CDKN1A (-10k, +10k from TSS)

library("p53retriever")
data(CDKN1A)
hits<-p53track(CDKN1A,seqname="CDKN1A")
p53plot(hits,0,20000)

Contact

[e-mail]

tomateba/p53retriever documentation built on May 31, 2019, 6:10 p.m.