Multiple protein accession number query Command LIne Blastp

Question

[john]

So I've scoured the internet and I couldn't find any documentation on how to format a txt file with multiple protein accession numbers.. As of right now, I have formatted like this:

AAF45826
AAF48069

The issue is it only blasts the first protein accession number. Does anyone know the proper format so that the program blasts every protein accession number?

Thanks in advance

Answer 1

[vkkodali_ncbi]

You can use Entrez Direct to download the sequences in fasta format on the fly like this:

blastp -query <(epost -db protein -input <acc_list.txt> | efetch -format fasta) -db <your_db>

The acc_list.txt file should contain valid protein accessions, one per line.