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Configure BLAST output?

I know this is a very specific question related to BLAST and Bioinformatics, but here it is:

I am trying to use standalone BLAST (I already downloaded it and tested it on the command line) to perform DNA sequence alignment (blastn). I need to provide both my own request file (fasta format) and my own database file (also fasta format).

The key is that I want the program to display only 2 fields, not the detailed reports that it usually displays. I need only the highest score and e value for alignment. The idea is that as soon as I work, I can wrap this in my own control program and automatically run it many times with different sequences of queries and record points and electronic values.

I know this is a long shot, but does anyone know how I can do this? Two obstacles for me are using my own database file and setting up the output.

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2 answers

it's actually simple: it blastallhas several command line options that will help you:

  • : -v 1 -b 1
  • : -m 8

- :

blastall -p blastn -i queries.fasta -d database -v1 -b1 -m8 > resultTable.txt

. , cut . , 1, 7 8 blastoutput

cut -d '\t' -f 1,7,8 < resultTable.txt

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Yannick , , , blastall - , , - . BLAST , .

blastall formatdb, fasta, BLAST. :

formatdb -i input_database.fa -p F

(input_database.fa.nhr, input_database.fa.nin, input_database.fa.nsq), blastall, ( .n*).

PS formatdb -h formatdb

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Source: https://habr.com/ru/post/1723581/

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