FAQ

What is it?
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.

Any dependencies?
This system uses the Delila system 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 genome browser.

What are the components of Delila-Genome?
The system has three main components: (A) The front-end (B)The server (C)Post scan tools
Fig. 1 gives a detailed architecture of the sytem.
Fig. 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/RXRα.
Fig. 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 the PXR/RXRα transcription factor.

How can this system be utilized?
Possible identification of transcription factor binding sites and mRNA splicing factors sites.
Prediction of alternate splicing sites.
Discovery of novel regulatory target genes.

What types of binding sites were scanned?
We have used this system to scan the human genome for transcription factors like PXR/RXRα, AHR, NF-kB p50/p65 and mRNA splicing factors like donors, acceptors, and SC35.

What software was used in building this system?
Server - Perl, Pascal, Bash
Front end - Java, HTML

On what systems will this software run on?
The 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).