Introduction

Bioinformatics is a relatively new interdisciplinary field that integrates mathematical sciences, computer sciences, and biology.  Our lab is developing  (adopting, modifying and inventing) Bioinformatics tools for genome analyses and gene ontology studies.  Gene ontology addresses Biological Process (Why is this, such as cell enlargement, being done?), Molecular Function (What kind of molecule is this? Enzymes or transcription factors?), and Cellular Component (Where is this located? Nuclei or Mitochondria?). 

 

We are building four modules -- Genome Analysis Modules, Database Module, Graphic Display Module and Web Interface Module -- which, after integration, will be made available in the public domain to serve the need of researchers.  The 11 high-end Sun Enterprise computers plus 11 storage arrays recently donated to us by Monsanto Company will drastically enhance our capability of performing genome analyses and providing web services.

Four Modules Being Developed in Shen Lab

Tools Developed in Shen Lab

Promoter Analysis

Due to the diligent work of several bioinformaticians, several Bioinformatics tools have been developed in our lab.  One of the programs is for "Promoter Structure Analysis and Display". This program can analyze thousands of promoters for the presence of a defined set of cis-acting elements. The color-coded bars display each class of cis-acting (e.g. responding to a given hormone) elements along with their positions and orientations, as shown in the following example.

 

 

This Figure displays the structures of four ABA-responsive promoters -- from barley (HvA1 and HvA2) and Arabidopsis (AtRd29B and AtRd29A) respectively-- and two GA-responsive promoters from barley (HvAmy32b encoding a low pI alpha-amylase and HvAmy46 encoding a high pI alpha-amylase). The numbers (eg. N84) indicates the distance between the two neighboring cis-acting elements and the arrow in a bar shows the orientation of that element.  The graph is drawn to the scale.

You may click any part of the figure to bring up a new webpage.  Then click each link in the new page to find out what this program can do.

Before an interactive webpage is launched, you may send your promoter sequences (in the multiple FASTA format) to me by email and we will send the analysis result to you via email too.

Protein Motif

Another program you may find useful to your research is the "Protein Motif Identification and Display", which can find putative signals such as those for subcelluar localizations or post-translational modifications.

 

You may click any part of the figure to bring up a new webpage.  Then click each link in the new page to find out what this program can do. The number of asterisk symbols following the name of an motif indicates how many over-lapped motifs represented by that bar--one for two motifs, two for three and so on. The graph is drawn to the scale.

Before an interactive webpage is launched, you may send your promoter sequences (in the multiple FASTA format) to me by email and we will send the analysis result to you via email too.