Setting E-Value In Blast

Question

[anika.menon22]

Hi,

Again I realize that its an easy question :). Could anyone tell me how to set e-value to 0.005 in Blastp?

[justinhaselbach]

In Local BLAST or at NCBI-BLAST [web-based] ?

[anika.menon22]

NCBI-blast. Thanks

Answer 1

[bioinfo]

This is not even a bioinformatics problem. Try to browse the NCBI blast interface properly especially the algorithm parameters section at the bottom. If you are using command line then just type -e 0.005 in your argument. I guess you didnt even try.

[anika.menon22]

Yes i did try and couldn't get the answer hence I posted the question here. But thank you for your reply. not everyone is smart like you :)

Answer 2

[justinhaselbach]

Okay, here we go. Go to the NCBI BLASTp Page; Expand [+] the "Algorithm Parameters (by clicking on the symbol); & in there the 3rd Parameter is Expect/ E- Value: by default NCBI uses 10; so you use whatever value you wish to ! Say: 0.005 ! Thanks,

[anika.menon22]

Thank you :) . i did exactly the same but it did not work. But alteast you have been kind to ans :)

[Hamish]

That looks like a bug, I suggest you contact the NCBI's BLAST help-desk ([e-mail]) and report the issue with the service.

Given a BLAST result on the NCBI BLAST web site you can simulate the effect of the E-value threshold by using the "Formatting options" menu (at the top of the page) to "Limit results" based on "Expect Max". This gives the same result as setting the parameter at submission.