[Bioperl-l] running remoteblast

[Wiepert, Mathieu]

Hi,
 
As Jason pointed out, you need to use the RemoteBlast module.  I think you may have missed the documentation (can't verify how up to date, but it looks current to me)
 
http://www.bioperl.org/Core/Latest/bptutorial.html#iii.4.1_running_blast_(using_remoteblast.pm <http://www.bioperl.org/Core/Latest/bptutorial.html#iii.4.1_running_blast_(using_remoteblast.pm> )
 
And there is also documentation in the header for the object, which can be viewed in the cvs repository at
 
http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/Tools/Run/RemoteBlast.pm?rev=1.17 <http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/Tools/Run/RemoteBlast.pm?rev=1.17&cvsroot=bioperl&content-type=text/vnd.viewcvs-markup> &cvsroot=bioperl&content-type=text/vnd.viewcvs-markup
 
(or just look at the object on your local machine with your favorite editor or text browser.
 
HTH,
 
-mat
 

-----Original Message-----
From: omid gulban [mailto:gulban at sickkids.ca]
Sent: Monday, December 01, 2003 1:13 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] running remoteblast


Hi,
 
I would like to know how to run a remoteblast query using bioperl modules. I have looked in the FAQs but the instructions provided were for StandaloneBlast. I followed the instruction by received the following message:
 

-------------------- WARNING ---------------------
MSG: cannot find path to blastall
---------------------------------------------------

I assume that you need to install blast on your local machine. 
 
I am new to Bioperl. I don't know what modules to use?
How can I run a simple blast querry using NCBI?
 
 
Thanks
 
ACGT

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