How many HSPs does blastn returns by default?
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3 months ago
langziv ▴ 20

Hi.

The input file is a multi fasta file. Does blastn returns one HSP per sequence? Can an HSP consist of multiple genes or a whole genome/assembly? Does it return multiple HSPs and writes them in separate lines in the output file?

blastn blast alignment hsp • 160 views
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3 months ago
Mensur Dlakic ★ 11k

It will return all HSPs with E-values below the cutoff. No, an HSP can be created only within a single, continuous sequence. Yes, a single sequence can have multiple HSPs that will be written separately in the output file.

You may want to go through search results for HSP blast meaning.

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