Application Name

Gene Detection Service Blanks

Summary

• Name: Gene Detection Service Blanks
• Contact Person: support-compss@bsc.es
• Access Level: public
• License Agreement: Apache2
• Platform: COMPSs
• Repository: ​Gene Detection Service Blanks

Description

The Gene Detection service offers the functionality to perform automatic functional analysis of the relevant genes of an aminoacid sequence using a combination of the Blast and Genewise Software and other bioinformatic services. More details about the algorithm can be found in [1]. Basically, the application is composed by 4 parts: Part A performs a format change of input data; Part B performs a search of similar aminoacid sequences; Part C performs the relevant gene search ; and finally, Part D perform the funtional analysis of the relevant genes. The number of parallel task varies depending on the number of similar sequences and the relevant genes found in every run and the number of concurrent runs invoqued in the service

Only for tutorial purposes.

Requirements

• Apache maven for building the software
• Blast 2.2.15
• Wise 2.2.0

Build instructions

mvn clean install -Dwise.location=</path/to/wise/> -Dblast.location=</path/to/blast/>

Execution instruction

This application is a webservice. To deploy it copy the following war files to an application server container

${basedir}/target/GeneDetection-1.0-SNAPSHOT.war

${basedir}/data/GeneDetectionGUI.war

${basedir}/data/Monitor.war

run the application server

References

[1] R. Royo, J. Lopez, D. Torrents, and J. Gelpi, “A Bio Moby - based workflow for gene detection using sequence homology,” in International Supercomputing Conference (ISC’08), Dresden (Germany), 2008.