haotu : an open lab notebook

2012/03/09

Make a minimal sized BLAST output file xml

Filed under: BLAST — S @ 07:07

The BLAST output txt/xml file can be huge. In order to make it smaller, especially for when dealing with many contigs, is to use the -b and the -v commands

-b

 Number of database sequence to show alignments for (B) [Integer] default = 250

-v

 Number of database sequences to show one-line descriptions for (V) [Integer] default = 500

blastall -p blastx -d xtropProtein12_03_08.fasta -i 2.fasta -e 2e-20 -b 0 -v 1 -o out2.xml

This produced BLAST output with 1 hit above 2e-20 and no alignments.

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