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Blast2GO

Description

blast2go website

This module enables the use of the Blast2Go 4Pipe command line software The Blast2GO Pipeline Version (B2G4Pipe) runs Blast2GO without graphical interface. The pipeline accepts BLAST and InterProScan results and parses the XML belonging to each sequence (provided in FASTA format). The program extracts GO terms to each obtained blast hit by mapping to existent annotation associations. An annotation rule finally assigns GO terms to the query sequence. Additionally you can add domain/motif based GO term obtained through InterProScan searches. Deduced GO terms are added to the BLAST based annotations, always taking into account the GO True-Path-Rule. The output files generated by B2G4Pipe are equivalent to the file generated by the desktop application. How to run with default properties: use the b2g4pipe wrapper, which is equivalent to "java -Xms64m -Xmx500m -cp $B2G4PIPE/:$B2G4PIPE/ext/: es.blast2go.prog.B2GAnnotPipe -prop $B2G4PIPE/b2gPipe.properties -v -annot -dat -img -ips ipsr -annex -goslim -wiki $B2G4PIPE/html_template.html" and only requires the input and output file names such as : -in input.xml -out results Additional wrappers are provided for various memory settings (See http://www.blast2go.com/b2glaunch/start-blast2go for a table of memory vs. number of sequences that can be annotated) such as b2g4pipe-1000, b2g4pipe-1500, b2g4pipe-2000, and b2g4pipe-4000. If you need to change the switches build your own appropriate command line. To use the HPC GO database with a graphical Blast2go interface configure your Blast2go installation and use the '10.13.20.209' database host (db1.ufhpc) with 'blast2go' user and 'blast2go' password. You will have to create an ssh tunnel to the database host as it's not accessible otside of the HPC cluster. * B2G4PIPE - internal Blast2go variable for installation directory location.

Environment Modules

Run module spider blast2go to find out what environment modules are available for this application.

Environment Variables

  • HPC_BLAST2GO_DIR - installation directory

Additional Usage Information

Database Releases

  • December 2011 - "b2g" database.
  • November 2012 - "b2g201211" database.
  • November 2013 - "b2g201311" database.
  • March 2015 - "b2g201503" database.

Using B2G4PIPE at UFRC

Please note that the Blast2Go team considers b2go4pipe obsolete and unsupported. If you need the results that the current Blast2Go software produces you should consider purchasing a license. You can use the database we host on HiPerGator with the Blast2Go GUI application running on your local computer or through OOD. As far as we know Blast2Go command-line tools still have node-locked licenses, so it is not feasible to run them on a computer cluster like HiPerGator. Keeping the above in mind it is still possible to run B2G4PIPE and generate Gene Ontologies for your BLAST data.

Below are considerations and modifications you need to make to have a successful run.

Blast2GO can not reach the Internet

  • This warning should be ignored. It's likely due to a server check b2go4pipe does at the beginning of a run.

Changed property MainGui.Workspace from results.annot to test_cit.annot /apps/blast2go/2.5.0-20120705/b2gPipe201503.properties (Permission denied)

  • It looks like you need a local copy of b2gPipe201503.properties. Copy it to your current working directory and use it when running B2GO4PIPE

Problem creating wiki file

  • html_template.html (No such file or directory):

  • See the default run example below. You have to provide the full path to the template file i.e. '-wiki PE/html_te$B2G4PImplate.html'

Can not parse BLAST XML because can not find information about the used version!

  • Since b2go4pipe has not been updated in years it likely produces an error when encountering newer BLAST versions in the BLAST xml file. Edit the xml file to change, for example,
 <BlastOutput_version>BLASTP 2.5.1+</BlastOutput_version>

to

 <BlastOutput_version>BLASTP 2.2.26</BlastOutput_version>

How to run with default properties

Use the b2g4pipe wrapper, which is equivalent to "java -Xms64m -Xmx500m -cp $B2G4PIPE/:$B2G4PIPE/ext/: es.blast2go.prog.B2GAnnotPipe -prop $B2G4PIPE/b2gPipe.properties -v -annot -dat -img -ips ipsr -annex -goslim -wiki PE/html_te$B2G4PImplate.html" and only requires the input and output file names such as : -in input.xml -out results

Additional wrappers are provided for various memory settings such as b2g4pipe-1000, b2g4pipe-1500, b2g4pipe-2000, and b2g4pipe-4000.

If you need to change the command line switches beyond the existing wrappers then you'll have to build your own appropriate command line.

Using HPC GO database from a graphical Blast2GO application

To use the HPC GO database with a graphical Blast2GO interface running locally on your computer:

  • Start an SSH tunnel, forwarding port 3306:

    • In your ssh client, type: ssh -L 3306:blast2godb.ufhpc:3306 user@hpg.rc.ufl.edu -N
    • Enter your password at the prompt.
    • The terminal will remain with no input command line, but any MySQL traffic (using port 3306) will be directed to the database server.

  • Configure your Blast2GO installation to use the UFRC database:

    • Select Tools menu and then DB Configuration
      1. DB Host: localhost
      2. DB Name: b2g201503
      3. DB User: blast2go
      4. DB Password: blast2go

Categories

biology, genomics