Using Blast2Go From The Command Line

Question

[Eric Normandeau]

Hi,

I am looking for a way of using Blast2Go on a remote server in a more or less FIRE AND FORGET manner. My idea is to use either a command line version of Blast2Go or an API that would permit me to use it on a server. So far, I have found neither.

Another approach I thought about was to have the server admin install X Window System capabilities to the server, plus a browser (like Konqueror) and the required java packages.

Maybe I am totally on the wrong track here and should resort to another approach, like a totally different automated annotation application.

Would you have any suggestions or comments concerning the following:

• Command line access to Blast2Go on a server
• Using X Window System (X11) and java on the server
• Switching to another application

As always, many thanks!

Cheers

Answer 1

[Lars Juhl Jensen]

Blast2GO has a command line version without GUI, which is meant for use in your own pipelines. It is called B2G4PIPE and is available from their download page. I have not used it myself, but it sounds to me like it should fit the bill.

Answer 2

[Sujai Kumar]

Am trying this right now and it seems to work fine.

• Get your blast results in xml format (I used NCBI's blast+ 2.2.25 suite):

  blastp -query proteins.faa -db nr -outfmt 5 -evalue 1e-3 -max_target_seqs 20 -out proteins.xml
  

• Install b2g4pipe235 (just tar gunzip it)

• Edit the properties in b2gPipe.properties (Most importantly, change the section on dbname etc to use the settings you would get from the GUI blast2go. These worked for me, but they might change in the future:

  // Conectivity to WebServices
  Webservice.url=http://blast2go.bioinfo.cipf.es/b2gws_axis2
  
  // GO and B2G-Mapping Database
  Dbacces.dbhost=193.144.127.204
  Dbacces.dbname=b2g_may10
  Dbacces.dbuser=blast2go
  Dbacces.dbpasswd=blast4it
  

• Run:

  java -Xms3000m -Xmx8000m -jar blast2go.jar -in proteins.xml -v -a -out MyAnnot -d MyAnnot.dat -p b2gPipe.properties
  

[upendrakumar.devisetty]

Hi,

I am new to blast2go and i am wondering where can i download the b2g4pipe235 file.