Question: How to run blastp selectively against plants & fungi in blast2.5.0+?
0
gravatar for mirza
2.3 years ago by
mirza80
India
mirza80 wrote:

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?

blastp blast+ • 999 views
ADD COMMENTlink modified 2.3 years ago by Farbod3.2k • written 2.3 years ago by mirza80
1

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

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Prasad1.5k

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

ADD REPLYlink written 2.3 years ago by mirza80
0
gravatar for Farbod
2.3 years ago by
Farbod3.2k
Toronto
Farbod3.2k wrote:

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

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Farbod3.2k

@Farbod Thanks for your suggestions.

ADD REPLYlink written 2.3 years ago by mirza80
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