[Biojava-l] Program ncbi-blastp Version 2.2.2 is not supported
Simon Brocklehurst
simon.brocklehurst@CambridgeAntibody.com
Tue, 26 Mar 2002 17:56:17 +0000
--------------EAF4B885DC0F83D07C359744
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Dave Waddell wrote:
> Is there any development being done in this area? Can I help?
>
> Thanks, Dave.
>
> Exception in thread "main" org.xml.sax.SAXException: Program
> ncbi-blastp Version 2.2.2 is not supported by the biojava blast-like
> parsing framework
>
Dave,
The code is "sort of" easy to understand if you're prepared to wade
through it. That is, it's not too hard to add support for new versions
(documentation is wanting). Feel free to go for it!
If you want to get going right away with using biojava, you can use
simply use a version of Blast that is currently suported by the
framework - many versions are available for download by ftp at:
ftp://ftp.ncbi.nih.gov/blast/executables/old
You want NCBI Blast version 2.0.11
Simon
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com
--------------EAF4B885DC0F83D07C359744
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit
<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
<body link="#0000FF" vlink="#800080" lang="EN-US">
<p>Dave Waddell wrote:
<blockquote TYPE=CITE><style>
<!--
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:purple;
text-decoration:underline;}
span.EmailStyle17
{font-family:Arial;
color:windowtext;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.25in 1.0in 1.25in;}
div.Section1
{page:Section1;}
-->
</style>
<div class=Section1>
<div class="MsoNormal"><span style='font-size:10.0pt;
font-family:Arial'><font face="Arial"><font size=-1>Is
there any development being done in this area? Can I help?</font></font></span></div>
<p class="MsoNormal"><span style='font-size:10.0pt;
font-family:Arial'><font face="Arial"><font size=-1>Thanks,
Dave.</font></font></span>
<p class="MsoNormal"><span style='font-size:10.0pt;
font-family:Arial'></span>
<p class="MsoNormal"><span style='font-size:10.0pt;
font-family:Arial'><font face="Arial"><font size=-1>Exception
in thread "main" org.xml.sax.SAXException: Program ncbi-blastp Version
2.2.2 is not supported by the biojava blast-like parsing framework</font></font></span></div>
</blockquote>
<p><br>Dave,
<p>The code is "sort of" easy to understand if you're prepared to wade
through it. That is, it's not too hard to add support for new versions
(documentation is wanting). Feel free to go for it!
<p>If you want to get going right away with using biojava, you can
use simply use a version of Blast that is currently suported by the framework
- many versions are available for download by ftp at:
<p><A HREF="ftp://ftp.ncbi.nih.gov/blast/executables/old">ftp://ftp.ncbi.nih.gov/blast/executables/old</A>
<p>You want NCBI Blast version 2.0.11
<p>Simon
<br>--
<br>Simon M. Brocklehurst, Ph.D.
<br>Head of Bioinformatics & Advanced IS
<br>Cambridge Antibody Technology
<br>The Science Park, Melbourn, Cambridgeshire, UK
<br><A HREF="http://www.CambridgeAntibody.com/">http://www.CambridgeAntibody.com/</A>
<br><A HREF="mailto:simon.brocklehurst@CambridgeAntibody.com">mailto:simon.brocklehurst@CambridgeAntibody.com</A>
<br>
</body>
</html>
--------------EAF4B885DC0F83D07C359744--