I would like to compare two bacterial genomes using tblastx for subsequent visualization in ACT (artemis).
Here is my tblastx command:
tblastx -db reference_genome -query query_genome.fas -out comparison.txt -outfmt 7 -num_threads 8 -evalue 1e-5
I got only 400 hits and all of them have evalues of 0.0 (blastn for example give me almost 8000 hits, and the evalue is variable).
I believe that something is filtering the results, but it is not clear to me.
Any ideas?
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fhsantanna
Did you try specify the -max_target_seqs parameter? According to my version (TBLASTX 2.2.29+), the number of output target sequences by default is 500, you should be able to increase it further.
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mark.ziemann
Yes, Mark. Later I figured out the problem. I was utilizing blast+ 2.2.27, which apparently has a bug.
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Blasting a sequence against itself also returns 400 hits.