Good morning, I'm aligning with blast some species, against all nt database to analyse the vegetables. However, in some cases we have species of animals mixed with vegetables and want only to detect the vegetable species. Normally, we would only expect to detect the vegetables only. But this is normal since we are using the all nt. So now, could anyone point me out, the way to detect only vegetables? Thanks for the help.

  • 1
    $\begingroup$ Cross posted at BioStars: biostars.org/p/421717 $\endgroup$
    – Joe Healey
    Feb 12 '20 at 10:51
  • $\begingroup$ vegetables are plants, meat are animals, you can filter nt to the taxonomic groups you are interested in $\endgroup$ Feb 12 '20 at 11:05
  • $\begingroup$ why was this question avaluated with -1? $\endgroup$
    – Sofia
    Feb 12 '20 at 15:55
  • $\begingroup$ -1 means it got downvoted, probably because a user did not appreciate the question, maybe because of lack of details, language, or simply because they found it is fun. I personally do not like the principle of downvoting questions at all, as it is utterly disrespectful. Still that is how SE works. Speaking of your question, please consider being more precise in the future. Use correct terminology (plant, not vegetable, animal, not meat) and also say that you want to do this remotely, not via the web browser as the user who gave an answer assumed. $\endgroup$
    – ATpoint
    Feb 12 '20 at 21:08
  • $\begingroup$ Hello Atpoint, thank you for the suggestions and I will do it. $\endgroup$
    – Sofia
    Feb 13 '20 at 10:42

Using the blast command line tool, you can limit your search to a specific taxon using the –taxids option.

So, in your case -taxids 3193 should limit your search to plants.

If you are using the ncbi blast webinterface, you can restrict your search by entering "plants" into the Organism field in the "Choose Search Set" section

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  • $\begingroup$ Yes, but I want to use that restriction remotely... $\endgroup$
    – Sofia
    Feb 12 '20 at 11:43
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    $\begingroup$ Ah okay, I edited my answer to include the option in the command line tool $\endgroup$
    – Wayne_Yux
    Feb 12 '20 at 12:45
  • $\begingroup$ Thank you Wayne_Yus for the help! It was really helpful and I'm sorry if my question description mislead you. $\endgroup$
    – Sofia
    Feb 13 '20 at 10:43

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