Why Do Blastall And Blast+ (Blastn) Give Different Results For What I Beleive Is The Same Search?

Question

[David M]

I've recently run two searches, one with blastall (from legacy blast) and one with modern blastn. Both versions are 2.2.25 (the most recent).

The blastall search is: blastall -i test.fasta -p blastn -d old_formatted_database -m 8 -e 1e-10

The blastn search is: blastn -query test.fasta -db new_formated_database -outfmt 6 -evalue 1e-10

Note that the two databases have each been created with the program's respective formatdb utility.

The blastn search yields 3 results, while the blastall search results in over 50. Why is this? I realize the programs themselves are not readily comparable, but I was under the impression that their output should be similar since they're based on the same scoring methods.

From a more theoretical point of view, shouldn't there be an exact number of hits matching a given query sequence and scoring scheme? Shouldn't these all be reported regardless of the blast approach used?

[Michael]

can you upload and share your data for reproducing this (meaning both databases and the test.fasta), or if not appropriate make another test.db? Otherwise, I would guess or hope that there are some different parameter defaults to explain this. Also, what happens if you use a query identical to the blastall query but using the legacy command wrapper in blast+?

[David M]

I can't upload the data, but I'll make a test DB later today. I did try running the query in the legacy wrapper, and I got a 3rd, different set of results (over 150 hits). I'm also curious about the defaults; I suspect this is where the difference arises. I was hoping someone here might have some insight into the differences in these defaults.

[Torst]

Was the query particularly short or long? Or the database huge? Because BLAST+ will automatically alter "-task" to enable megablast or blastn-short modes instead of regular blastn. Whereas BLAST has megablast as a separate application.

[Torst]

Also, low complexity filtering could be different between BLAST and BLAST+, limiting search results in one of them. Use "blastall -F F" and "blastn -dust no" to compare properly.

[Michael]

Any news on the test-case?

Answer 1

[Jon Binkley]

blast+ has a "task" option for blastn and blastp searches. Available blastn tasks are "blastn", "blastn-short", "megablast", and "megablast-dc". For some reason, the default task for blastn is not blastn, but megablast! So, to get it to work like your blastall search, your blast+ command should be:

blastn -task blastn -query test.fasta -db new_formated_database -outfmt 6 -evalue 1e-10

[Istvan Albert]

whoa! that's unexpected!