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Tblastx returning only 400 hits
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12 months ago
fhsantanna • 440
Brazil

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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Blasting a sequence against itself also returns 400 hits.

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12 months ago
mark.ziemann ♦ 1.2k
Australia/Mebourne/Geelong/Deakin

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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Yes, Mark. Later I figured out the problem. I was utilizing blast+ 2.2.27, which apparently has a bug.

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