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Old 10-23-2015, 02:12 AM   #1
scami
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Location: italy

Join Date: Sep 2010
Posts: 55
Default Search specific blast database regions

Hi there,

I am using blastn in command line. I have a genome and created a blast database out of it with makeblastdb
During the pipeline I am developing I need to blast some sequence versus specific chromosomes of the genome and not the entire genome. At the moment I use the command

blastn -query queryFile -db genomeDatabase -outfmt 6

Let's say that in the genomeDatabase file I have chr1, chr2, chr3 and so on. What can I add to my command to search my sequence versus just chr1 or chr2 and so on?
thanks for your help!
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