How to run blastp selectively against plants & fungi in blast2.5.0+?

Question

[mirza]

Hi, I have blast2.5.0+ and have downloaded nr database. Since, blast with the complete nr db will take months for a whole genome, how can I run blastp selectively against only plant and fungi data?

[Prasad]

in blast help check Restrict search or results section or from here in table C1. there are multiple option like gilist, seqidlist, negative_gilist etc

[mirza]

@Prasad Thank you for your suggestions. I'll try to use these options.

Answer 1

[Farbod]

Dear mirza, Hi.

You can use Diamond and do your search about 20,000 times faster than BLAST.

In addition, using BLAST2GO (NOT so fast), you can select the database you need (e.g Arabidopsis, etc) for your blast.

~ Best

[mirza]

@Farbod Thanks for your suggestions.