[Biodevelopers] XML BLAST

[Ela Hunt]

Hi,
1. Blast has an output option producing XML, -m 7

  -m  alignment view options:
0 = pairwise,
1 = query-anchored showing identities,
2 = query-anchored no identities,
3 = flat query-anchored, show identities,
4 = flat query-anchored, no identities,
5 = query-anchored no identities and blunt ends,
6 = flat query-anchored, no identities and blunt ends,
7 = XML Blast output,
8 = tabular [Integer]
    default = 0

2. I parsed it a while ago using a SAX parser, just to try it out, so my 
software is not robust, but it was easy. I think I had to add a top level 
node to the DTD, so that a bunch of results (each being a separate XML record 
but all in one file) could be read in as a tree. Possibly robust solutions 
are out there to be found.
Ela

-- 
_________________________________________________________________________

Ela Pustulka-Hunt MA MPhil BA PhD	Email: ela at dcs.gla.ac.uk
MRC Research Fellow			Phone: +44 141 330 6034
       				        Fax:   +44 141 330 4913
						
University of Glasgow, Department of Computing Science, 
8-17 Lilybank Gardens, Glasgow G12 8QQ, SCOTLAND
http://www.dcs.gla.ac.uk/~ela
_________________________________________________________________________