BlastViewer only relies on the management of well-formed XML files. XML what ? Well, you are certainly familiar with the standard text format of a Blast result: this is what you can see on all Blast servers around the world. This file can be read by a human being, however it is not as easy for a computer software. For that purpose, the creators of Blast have provided the bioinformatics community with two formats suited for software applications. They are ASN.1 and XML. Because of the Internet age, XML has become widely used, so BlastViewer is only capable of reading the XML files produced by Blast; if you have ever used Blast on the command-line, this is the '-m 7' output format.

As soon as you use either the NCBI or the EBI Blast server, a local installation of Blast (i.e. the command-line version of Blast) or an in-house WWWBlast server, you can easily obtain such an XML file. Please, refer to the BlastViewer manual for more information (see below).

Now, if you want to allow BlastViewer (or KoriBlast) to read data produced by any kind of sequence database search engines, you just have to produce result files that conform to the NCBI BlastOutput DTD or the EBI ApplicationResult XML schema.Here are the links:

EBI ApplicationResult schema: have a look at ApplicationResult.xsd

NCBI BlastOutput DTD: have a look at NCBI_BlastOutput.dtd and NCBI_BlastOutput.mod.dtd.

If you produce such a data file but you fail to open it with BlastViewer, please feel free to contact us to provide you with our help.

In addition to these standard XML data files, BlastViewer is capable of reading data files coming from the KoriBlast platform (actually, those files are XML formatted, but they are also compressed). By default, they have the '.zml' file extension.

(*) by default, the installation directory of KoriBlast is: 'c:\Program Files\KoriBlast' (Windows), '/opt/KoriBlast' (Linux) or '/Applications/KoriBlast.app' (MacOS X).