Delila-Genome is a system for identification, visualization and
analysis of protein binding sites in complete genome sequences.
What is the basis for
identification of the binding sites?
Shannon Information theory. Read about the application of information
theory to molecular biology at Dr.
Tom Schneider's page
This system uses the Delila
tools for the identification of potential sites over the
whole genome. From these potential sites, our tools select and visualize
those sites which are within or adjacent to expressed loci in the human
genome sequence. The visualization tools take advantage of the UCSC
What are the components of Delila-Genome?
The system has three main components: (A) The front-end (B)The server
(C)Post scan tools
1 gives a detailed architecture of the sytem.
2 shows screenshots of the HTML page generated by the system's
visualization tool (genvis) and
other websites linked to this HTML page. This page was generated from predictedbinding
sites on chromosome 1 for the transcription factor PXR/RXR
3 shows screenshots of scandiff
(a post scan tool to compare the results of genome scans with multiple
versions of the weight matrix) results around the gene CYP3A4 for
How can this system be utilized?
Possible identification of transcription factor binding sites and mRNA
splicing factors sites.
Prediction of alternate splicing sites.
of novel regulatory target genes.
What types of binding sites were
We have used this system to scan the human genome for transcription
factors like PXR/RXR
α, AHR, NF-kB p50/p65 and mRNA
splicing factors like donors, acceptors, and SC35.
What software was used in building
Server - Perl, Pascal, Bash
Front end - Java, HTML
On what systems will this software
server should work on all major Linux versions but it can be
ported to Solaris with little or no modifcations. The front-end should
work with all systems supporting Java (1.2 or higher versions).