<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<META content="MSHTML 6.00.2800.1276" name=GENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=#ffffff>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=562250613-02122003>Hi,</SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=562250613-02122003></SPAN></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN class=562250613-02122003>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)</SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=562250613-02122003></SPAN></FONT><FONT face=Arial color=#0000ff
size=2><SPAN class=562250613-02122003></SPAN></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN class=562250613-02122003><A
href="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</A>)</SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=562250613-02122003></SPAN></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN class=562250613-02122003>And
there is also documentation in the header for the object, which can be viewed in
the cvs repository at</SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=562250613-02122003></SPAN></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN class=562250613-02122003><A
href="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">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</A></SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=562250613-02122003></SPAN></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN class=562250613-02122003>(or
just look at the object on your local machine with your favorite editor or text
browser.</SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=562250613-02122003></SPAN></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=562250613-02122003>HTH,</SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=562250613-02122003></SPAN></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=562250613-02122003>-mat</SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=562250613-02122003></SPAN></FONT> </DIV>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Original Message-----<BR><B>From:</B> omid gulban
[mailto:gulban@sickkids.ca]<BR><B>Sent:</B> Monday, December 01, 2003 1:13
PM<BR><B>To:</B> bioperl-l@bioperl.org<BR><B>Subject:</B> [Bioperl-l] running
remoteblast<BR><BR></FONT></DIV>
<DIV><FONT face=Arial size=2>Hi,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>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:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2><BR>-------------------- WARNING
---------------------<BR>MSG: cannot find path to
blastall<BR>---------------------------------------------------<BR></FONT></DIV>
<DIV><FONT face=Arial size=2>I assume that you need to install blast on your
local machine. </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I am new to Bioperl. I don't know what modules to
use?</FONT></DIV>
<DIV><FONT face=Arial size=2>How can I run a simple blast querry using
NCBI?</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Thanks</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>ACGT</FONT></DIV></BLOCKQUOTE></BODY></HTML>