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How to used extraction above 90% identity with blastp?

I used command this

$ blastp -query file.fa -db dbfile.fa -outfmt "7" -evalue 1e-4 -out outfile.fa

But out file is a lot of information.

I need only above 90% identity information.

How to used extraction above 90% identity with blastp?

blastp blast protein identity extract
• 4,658 views • link
updated by reany • reany • written by ioer0417 • ioer0417

1 answer

The third column of your output file is the percent identity (pident), you can use awk to filter according to it:

awk '$3>=90' outfile.fa

And you would probably want to change the output file from outfile.fa to outfile.txt since it's not a fasta file.

• 0 views • link
written by Asaf Asaf

Thank you!

I have another question.

Can I?

I need a file like data1.

I want to files like data2, data3 is delete.

How can I try?

My result file information this

data1

Query: XP_1234

Database: data.fasta

Fields : query

1111 hits

XP_1234 XP_1234 100.00

data2

Query: XP_2345

Database: data.fasta

Fields : query

1231 hits

XP_2345 XP_2345 100.00

XP_2345 XP_3456 100.00

XP_2345 XP_4567 94.00

data.3

Query: XP_3456

Database: data.fasta

Fields : query

2343 hits

XP_3456 XP_2345 100.00

XP_3456 XP_6783 94.00

XP_3456 XP_8362 92.33

• 0 views • link
written by ioer0417 • ioer0417

I'm sorry, I couldn't understand you

• 0 views • link
written by Asaf Asaf

Asaf is a good answer, but in case you want to have this filtering with blast alone, you can use the parameters:

 -perc_identity <Real, 0..100>
   Percent identity
 -qcov_hsp_perc <Real, 0..100>
   Percent query coverage per hsp
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updated by Istvan Albert Istvan Albert • written by h.mon h.mon

You're right although I've seen some cases in which this filtering failed, maybe they fixed it in the new version.

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written by Asaf Asaf

As I understand, all blast filters are applied at an early stage of the algorithm, which means using the blast arguments may produce different results from filtering the output afterwards. There is an excellent series of posts at the blog Blasted Bioinformatics!?, e.g., What BLAST's max-target-sequences doesn't do. Due to these potential differences, it is often recommended to perform blast with "lax" parameters and filter the results afterwards.

• 0 views • link
written by h.mon h.mon

Exactly, thanks for the references, I had a vague memory of this explanation.

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written by Asaf Asaf

so why blastn have these parameters while blastp do not have parameter "-perc_identity" ?

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written by reany • reany

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