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infernal [2017/11/28 22:08] (current)
jokinsey Created Infernal Documentation
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 +====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''​.
infernal.txt · Last modified: 2017/11/28 22:08 by jokinsey