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BLAST multiple staxids
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19 months ago
Sri Lanka

I am using following output format to get my blastp output:

-outfmt, 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids

However, I get multiple values for staxids. I wonder why/what are they? Because I was expecting only one taxonomy ID of the subject. I cannot find this on BLAST documentation

Look at this example: https://ibb.co/9ZzJd9z

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What is the different between those two? How can a subject can have multiple Taxonomy IDs?

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15 months ago
gb • 780

From the help page:

staxid means Subject Taxonomy ID
staxids means unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)

So you can use staxid instead of staxids

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I agree. Thanks! But still I am curious about how we can get multiple Taxonomy IDs when we use staxids option

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I think I do not have the exact explanation for you but look up the taxonids. In your case the protein comes from a Escherichia coli (562) which is a species rank, and Escherichia coli 3-105-05_S1_C2 (1444084) which is the same species but a certain strain. So I think it has something to do with taxonids that have the same species but an extra strain number or code.

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Yes, I also had a look exactly on those TaxIDs and came to understanding as you. But now I think, may be other strains on the E coli also have the same sequence, that is why I get multiple TaxonomyIDs

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