[Biojava-l] Blast XML output problem with multiple sequences

[Ashika Umanga Umagiliya]

Hi guys,


I have a question with blastall. I use blast-2.2.18 on debian linux.
I execute 'blastall' from my java application.I use m -7 parameter to 
get the result as an XML file.

When my input file has more than one sequences like ,
 >id 1
ytfgqgtk
 >id 2
leikrkr


my output xml file actually contains two separate XML files appended 
together , like :

<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" 
"NCBI_BlastOutput.dtd">
  <BlastOutput>
   ..
   ..
  </BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" 
"NCBI_BlastOutput.dtd">
  <BlastOutput>
   ..
   ..
</BlastOutput>


How can i get my results in one XML file,so that i can process it easily?

Thanks in advance,
umanga