Blast Output Into Jsp/Html
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11.6 years ago
Yann ▴ 70

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 • 4.3k views
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parsing XML and echoing it ? there is no need for BioJava here.

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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 ?

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Any particular reason not to use BioJava?

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

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11.6 years ago

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

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11.6 years ago
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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.

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