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Blast Output GraphicLARTS and BLAST: Overcoming Complexity
Patches for BLAST
NCBI recently reworked the XML output produced by the BLAST program.    The blastall program currently outputs a BlastOutput data structure in XML when the XML (-m 7) output option is selected.  Selecting either of the ASN.1 output options (-m 10 or -m 11) results in the output of a SeqAlign data structure in ASN.1 binary or text.
We have modified the December 31, 2008 version of the NCBI Toolbox to produce the BlastOutput data structure in ASN.1 binary or text format.  Choose "-m 12" for text or "-m 13" for binary output of BlastOutput in ASN.1. 
LARTS parses ASN.1 BlastOutput in either binary or text format.  Please contact us if you need a custom filter. See our consulting page for more info.
The local alignment gif is still available through the -T (Produce HTML) option.
While you use NCBI BLAST, you may find certain functions ought to be enhanced either for greater speed or ease of use.  LifeFormulae™ patches allow support for generating local GIF images of the alignments on several computer platforms and we offer them to you without charge.
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