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Local Blast Output Format

Local Blast Output Format - Bioinformatics

Local Blast Output Format - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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Old 04-04-2010, 09:36 PM
Pipette Filler
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Default Local Blast Output Format



Hi,

I created a local blast tool with the new version of ncbi blast 2.2.23+. I want the output file in xml format, that corresponds to option 5, with a specific number of descriptions. Everything goes well except it appears more results than the number I specified with the command num_descriptions. My objective was to obtain the best 5 matches for each sequence. This works for a txt or html output file but not for xml.

What I wanted to know is if it is possible to specify the number of matches when we want the xml output format.

The command that I'm using:
blastx -query "C:\DataBase\query.fasta" -db "C:\DataBase\uniprot_sprot" -num_descriptions 5 -evalue 0.00001 -outfmt 5 -out "C:\DataBase\blast.xml"
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Old 04-05-2010, 02:30 PM
Pipette Filler
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Default Re: Local Blast Output Format

I found out that with the -max_target_seqs command I get a shorter list of matches...

thanks anyway,
Sara
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