Bioinformatics@AU-KBC have put out an software into Open Source

Details about the release is given below:

Bioinfotracker - Functional Genomics Application Server

Functional Genomics is one of the hot area in Bioinformatics which deals with finding biological function for the given input in terms of nucleotide or protein sequence. As on the date totally 450 genome projects sequence is available on the internet. Assigning function is very important for drug discovery process to find out right drug target. But the current database shows 50 % of functions for any of the organisms and remaining functions indicated as hypothetical proteins. To maximize the functionality, different tools are available (25 tools) in different web sites with different input and output formats.To analyze one sequence ,many operations are required.

To avoid the above said problem , many tools are integrated on one platform with easy input and easy output analysis operations.This Functional Genomic Tool (FGT) is an aid in functional analysis of entire genome in-silico. Submitting a gene or protein sequence to multiple sites such as XCOGITOR, WUBLAST, INTERPRO, PFAM etc for sequence analysis and aggregating together the returned results is a tedious task. This tool takes the burden off the user by automating this task of fetching and aggregating sequence analysis results from many sites. BLAST results will be analyzed in background and correct function can be extracted.To prevent browser time-out due to the long time required to fetch the result, Ajax has been used to fetch asynchronously. The tool has added ability of generating PDF research paper report of the aggregated results.Web hosting In addition to the above, the tool also contains Google search and other functionalities to get more information about the function.

Description

This Ajax based application server is written in Perl and Javascript. Installation is minimal, a web client page with associated Javascript files and two Perl server programs at the server machine. A bundle of Perl Modules (listed below) also need to be installed at the server machine. Once installed the application can be accessed and run at any Javascript enabled browser.

People

Dr.G.Ramesh Kumar
Research Scientist
AU-KBC Research Centre

R.Sathish Kumar
Project Engineer
NRCFOSS

Methodology used:

A user can paste a list of Gene IDs or a set of sequences in FASTA format and submit the jobs in the client browser. The Ajax engine at the browser sends the desentupidora data to the application server. If it is Gene IDs, then the respective Gene sequences are fetched from Genebank by the application server. In case of raw gene sequences this step is side stepped pariuri sportive. The sequences are then submitted by the server to WUBlast,Interpro,COG and PFAM sites respectively as follows:

COG and PFAM: Submit the custom term papers sequences and parse and analyze (using a host of parameters) the returned HTML (otimização de sites) results to extract the relevant information

WUBLAST and InterPro: Submit the sequences using the EBI SOAP services and poll the web services until the results arrive. Parse and analyze the output XML to extract the relevant information.Chris Harrisessay topics

These data are aggregated at the server and sent back to the client browser where the Ajax engine builds up the table of aggregated results. A PDF icon when clicked can produce a PDF report of the acompanhantes results

Application Features:

Interface: Ajax based Web Application Server

License: GNU General Public License (GPL)

Limitations on the number of sequences that can be submitted: No.

Sites aggregated (can be scaled up with no restriction):

1. http://www.ncbi.nih.gov/COG
2. http://pfam.janelia.org
3. http://www.ebi.ac.uk/Tools/webservices/WSWUBlast.html
4. http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html

Supported Browsers:

Mozilla Firefox 2.0+
Internet Explorer 5.5+

Programming Language: Perl,Javascript

Requirements:

Javascript enabled in the client browser. The following Perl modules are required at the server machine:

LWP::Simple
CGI
JSON
IO::String
Bioperl
HTML::TreeBuilder?
HTML::TreeBuilder::XPath
XML::Xpath
SOAP::Lite
Time::SoFar?
PDF::API2
PDF::Table

Demo at http://biotool.nrcfosshelpline.in (grafica)

Download Bioinfotracker at http://nrcfosshelpline.in/smedia/images/downloads/fgt.zip