Ligand database Consultation tool
This project has been done during my postgrade degree specialising in Bioinformatics (DESS Bioinformatique) at Lille University on a period of one month. It was in collaboration with Sabine Carnet, another student.
The Project
The goal of this projet is to develop a consultation tool of the Ligand database from the KEGG bank. The application was supposed to permit four services (abstract) :
- Enzymatic function consultation with differents informations
- List of enzymes appearing in a given metabolic pathway
- Pattern (motif) finding in the sequence of proteins having a given enzymatic function
- Find a given pattern (motif) in a given sequence
Project parts
The project is divided in two parts:
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The administration part:
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Retrieving the ligand database and converting useful information in XML format.
A Perl script reads the ligand database file and creates a file in XML format. -
Filling the local database.
A Java parser reads the created XML file and does update queries to a local database.
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Retrieving the ligand database and converting useful information in XML format.
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The user part:
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The user interface for local database consulting.
We used the Java Server Page (JSP) technology for a web interface. So, we have a Tomcat server to create pages dynamically.
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The user interface for local database consulting.
Project presentation
This project has been concluded by an oral presentation in french and a report in french too. The presentation can be download from here (french). The report in french is available in postscript (compressed with tar/gzip about 1.5mo) and pdf (about 1.2mo) format made with LateX.
The project has been develop with the Sun Java J2sdk 1.4.2_03.
The project has been tested under GNU/Linux (Debian - Mandrake) and Microsoft Windows XP (with cygwin (a Linux-like environment for Windows)) using the last version of postgreSQL. The project may not work on older versions.
Project files
Project files can be found here (documentation and comments in French, tar/gzip format about 3Mo, thanks to the agreement of the co-developer Sabine Carnet). See the README file for installation information.
Project demonstration
Not available anymore/ upon request back online.
The project can be tested by this link -- Be patient, the project is hosted on my personal computer, so the connection can be slow and connection can be lost due to dynamic IP address.