0
$\begingroup$

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.

$\endgroup$
  • 1
    $\begingroup$ Cross posted at BioStars: biostars.org/p/421717 $\endgroup$ – Joe Healey Feb 12 at 10:51
  • $\begingroup$ vegetables are plants, meat are animals, you can filter nt to the taxonomic groups you are interested in $\endgroup$ – Chris_Rands Feb 12 at 11:05
  • $\begingroup$ why was this question avaluated with -1? $\endgroup$ – Sofia Feb 12 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 at 21:08
  • $\begingroup$ Hello Atpoint, thank you for the suggestions and I will do it. $\endgroup$ – Sofia Feb 13 at 10:42
1
$\begingroup$

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

enter image description here

$\endgroup$
  • $\begingroup$ Yes, but I want to use that restriction remotely... $\endgroup$ – Sofia Feb 12 at 11:43
  • 1
    $\begingroup$ Ah okay, I edited my answer to include the option in the command line tool $\endgroup$ – Wayne_Yux Feb 12 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 at 10:43

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.