Only One Blast Result Per Query (Lowest E-Value)
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5.7 years ago
gtasource ▴ 60

I'm BLASTING to get gene names, and am only interested in the lowest E-value BLAST result for each query. From there, I'm looking to extract the gene name. How can this be done? I'm using the online server version of BLAST, but can easily transition to Linux.

BLAST • 2.0k views
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In command line, local Blast :

-max_target_seqs 1

On Blast API this should be the Algorithm parameters > General Parameters > Max matches in a query range

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Question. I recently read this article: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty833/5106166?redirectedFrom=fulltext

Does max_target give the lowest e-value? Or just any result that matches reaches the threshold.

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Hum interesting article, I would say, try the parameter on a well known dataset, if you get what you had expected, go ahead. If not, you can also filter the output yourself using bash command, python, perl etc...

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have a look at these ongoing threads :

I couldn't reproduce the problem of max_target_seqs

Misunderstood parameter of NCBI BLAST

that one you thus most likely should not set. Just ask any number and then filter the output afterwards to select the one with the lowest e-value

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