Question: Blast Output Into Jsp/Html
1
gravatar for Yann
9.6 years ago by
Yann70
Geneva
Yann70 wrote:

I would like to display a blast result in a jsp or html by parsing the xml result of blast without using BioJava? how can I do that?

blast • 3.9k views
ADD COMMENTlink written 9.6 years ago by Yann70
1

parsing XML and echoing it ? there is no need for BioJava here.

ADD REPLYlink written 9.6 years ago by Pierre Lindenbaum131k

What's the provenance of your blast result ? is it a DOM document in memory ? or is it a flat file stored on your computer ? Do you just want to print the XML in some HTML or do you want to redirect the user to the blast-XML file ?

ADD REPLYlink written 9.6 years ago by Pierre Lindenbaum131k

Any particular reason not to use BioJava?

ADD REPLYlink written 9.6 years ago by Niallhaslam2.3k

Do you real need to use the XML format? You could simply echo the default text format.

ADD REPLYlink written 9.6 years ago by Fred Fleche4.3k
3
gravatar for Istvan Albert
9.6 years ago by
Istvan Albert ♦♦ 85k
University Park, USA
Istvan Albert ♦♦ 85k wrote:

You can easily format an XML document into any other format via an XSLT stylesheet. You can even do it as a static page transformed directly in the browser with XSLT.

Find one of the many tutorials

ADD COMMENTlink written 9.6 years ago by Istvan Albert ♦♦ 85k
3
gravatar for Pierre Lindenbaum
9.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:
ADD COMMENTlink written 9.6 years ago by Pierre Lindenbaum131k
1
gravatar for Michael Schubert
9.6 years ago by
Cambridge, UK
Michael Schubert7.0k wrote:

Have you looked at the built-in BLAST HTML output?

> blastn -help | grep -A1 html
 -html
   Produce HTML output?

> blastn -version
blastn: 2.2.24+
Package: blast 2.2.24, build Aug 12 2010 17:47:58

This applies not only to blastn but the other programs as well. There is also wwwblast for the older version of the NCBI tools.

ADD COMMENTlink modified 13 months ago by RamRS30k • written 9.6 years ago by Michael Schubert7.0k
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