batch blast programme

Question

[Eva_Maria]

Hi every one I want to do a batch standalone blastn with this command

blastall -p blastp -d database.fasta -i aa.fasta -m 8 -e 1e-5 -o aa

I have more than 4000 inputs and I want out put respect to input name as I shown in the above command. How to do this?

Answer 1

[venu]

You can loop above command over each file. Search google for 'bash for loop'

[Ram]

Start with this. Then look to parallelize using GNU parallel or any other similar hardware backed parallelization. Running 4000 files in a loop is a bit daunting for anything advanced, such as tweaking performance or debugging.

[biocyberman]

You are using blastall which belongs to the outdated version of BLAST. Consider using BLAST+ package.

Answer 2

[Eva_Maria]

thank you for your comments

I found a solution for this

I wrote a code as below and it works

FILES=/home/ashok/Desktop/blast_batch/a/*
for f in $FILES
do
 blastn -db da.fasta -query "$f" -evalue 1e-5 -outfmt 6 -out "$f".out
done