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GIIRA is an open-source Java-based application that is designed to identify gene
regions in a genome based on a RNA sequence mapping and mapped reads. GIIRA also
automatically predicts gene isoforms and eukaryotic genes. The source code is
distributed under the GNU General Public License.
Features
– GIIRA can predict gene regions based on a RNA sequence mapping of two or more
Seqreads or a RNA-Seq mapping.
– GIIRA can identify gene isoforms.
– GIIRA has functions for generating maps for RNA-Seq read mapping and variant
detection.
– GIIRA can identify putative protein coding regions in a genome based on
information from a protein-encoding gene database.
– GIIRA provides an option to estimate and calculate the false-positive rate of
gene prediction based on gene length, number of reads and the number of
predictions.
Installation
If you do not have a Java JDK installed, it can be found at
GIIRA can be installed from a zip file and copied to a directory of your
choice. The files needed to run GIIRA are:
1) GIIRA.jar: This is the GIIRA application.
2) giira-data.jar: This is a data model of giira and includes some Java classes
of the data model.
3) giira.jar: This is the giira data model
4) dbi.jar: This is the database interface. It is used for the Seqreads and the
RNA-Seq reads mapping to a database.
5) ui.jar: This is the GUI.
To use the giira application with Java, there are two methods available. Either
use the user option to start GIIRA with a Java command or start GIIRA through
an executable file. If you choose to use the command line option, you have to
specify the path to the directory that contains the giira application and the
giira data model. After you run the command, you have to change into the
giira data directory and to extract the giira.jar file from the zip file. After
you extract the giira.jar file
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