====Infernal====

Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. You can find more information about Infernal [[http://eddylab.org/infernal/|here]].

====Environment Setup====

To use Infernal the modules for its software and other dependencies need to be loaded first. The easiest way to do this is editing your ''.bashrc'' file in your ''$HOME'' directory, by adding the lines below. You may have to restart your session for this to take affect.

<code>
module load impi/5.0.0
module load gcc/4.9.1
module load infernal
</code>

Then in your ''$HOME'' directory create a directory to submit your Infernal jobs from. Copy the tutorial folder, provided by Infernal, to the directory you just made in your ''$HOME'' directory.

<code>
razor-l1:jokinsey:~$ mkdir INFERNAL-JOBS
razor-l1:jokinsey:~$ cd INFERNAL-JOBS/
razor-l1:jokinsey:~/INFERNAL-JOBS$ cp -r /share/apps/bioinformatics/infernal/infernal-1.1.1-linux-intel-gcc/tutorial .
</code>

If you see a folder named ''tutorial'' in the submission directory you created then you are ready to run the example.

====Example Job====

In the submission directory for you Infernal jobs create a file named ''infernal.pbs'' with the information below. This is a ''PBS'' script that will be submitted to run the test job.

<code>
#!/bin/bash
#PBS -N infernal
#PBS -q tiny12core
#PBS -j oe
#PBS -o infernal.$PBS_JOBID
#PBS -l nodes=1:ppn=12
#PBS -l walltime=0:05:00

cd $PBS_O_WORKDIR
cp -r  tutorial /scratch/$PBS_JOBID
cd /scratch/$PBS_JOBID

cmbuild tRNA5.cm tutorial/tRNA5.sto

cmcalibrate --forecast tRNA5.cm
cmcalibrate tRNA5.cm

cmsearch -o tRNA5.cmsearch.out tRNA5.cm tutorial/mrum-genome.fa

mkdir $PBS_O_WORKDIR/infernal.$PBS_JOBID
cp -r . $PBS_O_WORKDIR/infernal.$PBS_JOBID
</code>

This script is first running ''cmbuild'' to build a covariance model using the alignment file provided with the tutorial. Then using ''cmcalibrate'' calculates the ''e-values'' needed to search the database. Finally it searches the sequence database provided by the tutorial, and stores that output to the file ''tRNA5.cmsearch.out''. This tutorial follows the example provided by Infernal, which you can find [[http://eddylab.org/infernal/Userguide.pdf|here]].

All that's left to do is submit the job.

<code>
razor-l1:jokinsey:~/INFERNAL-JOBS$ qsub infernal.pbs
</code>  

You can find the output located in the folder ''infernal.$PBS_JOBID''. If you need to review the standard output when the job was ran, it will be located in the file ''$PBS_JOBID.OU''.