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Hello, I am using blastn -remote option in terminal. But the results of evalues are different from online. In remote option evalues are approximately 3 times bigger than the online results. For example in online blast the result of e value 4.4 but in terminal by using remote option it is 12.
The commanline is:
blastn -query seq.fa -db nt -remote -task blastn-short -evalue 12 -qcov_hsp_perc 55 -word_size 11 -dust no -entrez_query "Oryctolagus cuniculus" -out result_seq.txt
Also i am using entrez_query for my specific organism but it also takes different organisms i didn't understand why did it take
Could you please help me to solve my problem?
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Thank you for the note :)
it is a known issue that the online version of blast behave a little bit different from the standalone ones.
Do check that you have to same version running local as offered online by NCBI, as well as mimick as good as possible the settings they use online.
A side note: e-values of 4.4 or 12 don't really matter, they are in fact both kinda pointless.
I am using same version both but thank you for the tip i'll try to mimick all the settings. Yes the evalue that i gave is pointless but it also turned significant evalues to meaningless.
That is likely because of the size/content of the database being searched against.