Hi, I am trying to do a tblastn search within a perl script.

 # one genome one query unix command
 my ($failcheck) = system(“tblastn -query -db -genome -out output.blast.tab”);
 die(“Error: could not execute system command\n”) if ($failcheck != 0);

My main question is how do I change my unix command so that I can go through a list of query and genome sequences and return the tblastn results for each?

Eventually I plan to look for sequences that I expect to find in the protein searches, which are similar to those found in close relatives of the genome I am searching. Although this may not be relevant to the question above.

In reply to tblastn unix by Nicpetbio23!

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