Exonerate

Description
	Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.
Site	Version (Latest: v2.2)	Notes
ngs.rl.ac.uk	v1.4.0

License

Exonerate is licensed under the LGPL.

Users of this application should credit the code authors and the NGS accordingly and where applicable the specific site where the code is installed, when publishing work using NGS resources.

Running Exonerate on the NGS

Exonerate has a range of programs shown below:

• Programmes:

exonerate      fastaannotatecdna  fastacomposition  fastahardmask  fastaoverlap   
fastasoftmask  fastatranslate     exonerate-client  fastachecksum  fastadiff    
fastaindex     fastareformat      fastasort         fastavalidcds  exonerate-server
fastaclean     fastaexplode       fastalength       fastaremove    fastasplit     
ipcress        fasta2esd          fastaclip         fastafetch     fastanrdb      
fastarevcomp   fastasubseq  

The example input filea aadnafra.fsa and humanDNA2.input can be found here:

gsiftp://ngs.rl.ac.uk:2811/apps/exonerate/examples/aadnafra.fsa
gsiftp://ngs.rl.ac.uk:2811/apps/exonerate/examples/humanDNA2.input

• Submission Using the UI/WMS

  To submit an Exonerate job via the WMS, login to the UI and create a JDL file as below, replacing your ngs ID on the UI for ngsxxxx, then submit using:

  glite-wms-job-submit -o jobIDs -a exon.jdl

  Type = "Job";
  JobType = "Normal";
  Executable = "/usr/ngs/EXONERATE";
  Arguments = "exonerate --model coding2coding aadnafra.fsa humanDNA2.input";
  StdOutput = "exonerate_res.out";
  StdError = "std.err";
  InputSandbox = {"aadnafra.fsa","humanDNA2.input"};
  InputSandboxBaseURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/exonerate";
  OutputSandbox = {"std.err","exonerate_res.out"};
  OutputSandboxBaseDestURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/exonerate";
  Requirements = Member("NGS-UEE-EXONERATE", other.GlueHostApplicationSoftwareRunTimeEnvironment);
  #Rank = other.GlueCEStateFreeCPUs;
  ShallowRetryCount = -1;

  • This runs the default version at any site. To run the 1.4 version use EXONERATE_1_4 instead of EXONERATE
  • The stdout file, exonerate_res.out, and stderr file, std.err, will be automatically returned to your work directory on the NGS UI machine, set here to 'exonerate'.
  • To use a different program, substitute for 'exonerate' in the Arguments= section one of the programs listed above, but keep 'Executable = "/usr/ngs/EXONERATE";' line.
• NGS Web Portal Submission

  After logging in to the NGS portal, select the "exonerate" template under the " bioinformatics" category and make the amendments appropriate for your specific job. Read the description page of the template for further details.

• Submission Using Globus

  Eg To submit an Exonerate job use the following command (one line. You should not include the backslashes):

  globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf \ '&(executable=/usr/ngs/EXONERATE_1_4) \ (arguments= exonerate --model coding2coding aadnafra.fsa humanDNA2.input) \ (jobType=single)(stdout=exonerate_res.out)'

   

Further Information

• Documentation for Exonerate