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News: -max_target_seqs 1 in NCBI standalone BLAST does not do what you think it does

To our surprise, we have recently discovered that this intuition is incorrect. Instead, BLAST returns the first N hits that exceed the specified E-value threshold, which may or may not be the highest scoring N hits. The invocation using the parameter "-max_target_seqs 1" simply returns the first good hit found in the database, not the best hit as one would assume.

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blast
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updated by Ram Ram • written by 5heikki 5heikki

1 answer

two related posts:

(solved) I couldn't reproduce the problem of max_target_seqs

Misunderstood parameter of NCBI BLAST

and I also want to add that there is a similar issue with other 'filetering' parameters: E-value threshold, num_alignemnts , ....

• 1 views • link
written by lieven.sterck lieven.sterck

My bad for not noticing the previous posts. Anyway, I think this issue deserves a lot of visibility. Like one of those previous posts could be a sticky until NCBI does something about it..

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written by 5heikki 5heikki

+1 for the "deserves a lot of visibility" !

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written by lieven.sterck lieven.sterck

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