Ability to match parameters of BLAST as per the web app

[Vinayak Kulkarni]

Hello,
This request is to make the params of BLAST match exactly that of the web app (or an ability to pass them as xargs to the code)

This is an example of params sent by the code today:

Program	blastn
Word size	28
Expect value	10
Hitlist size	100
Match/Mismatch scores	1,-2
Gapcosts	0,2.5
Low Complexity Filter	Yes
Filter string	L;m;
Genetic Code	1

and these are the params if BLAST is done on the web directly

Program	blastn
Word size	11
Expect value	0.05
Hitlist size	100
Match/Mismatch scores	2,-3
Gapcosts	5,2
Low Complexity Filter	Yes
Filter string	L;m;
Genetic Code	1

Thank you very much

[Laura Luebbert, Ph.D.]

Hi Vinayak, thanks for reaching out. gget currently matches the standard settings for megablast (on by default). It looks like the settings from the web you posted below are the standard settings for blastn without megablast. One exception is the expect value which was originally set to 10 as default (reference), but NCBI seems to have changed it to 0.05 (the expect value can already be modified by the user). I'll work on adding more arguments to adjust all of the options manually.

Could you please post your gget version, gget blast call, and how you returned the parameters?

[Vinayak Kulkarni]

Thank you Laura for a quick response. I was able to recreate near identical params to online version following your prompt.
Thank you for such a useful piece of software!