Hello all,

I am trying to establish a core proteome of A. baumannii, ie the proteins all of the strains have in common. I have multiple .fasta proteome files.

What would be the most appropriate way of going about this? would this do the trick?:

blastp -query query.fasta -db db -out output.txt -outfmt "6 qseqid qlen sseqid  salltitles pident mismatch gapopen qstart qend qcovs  sstart send evalue bitscore" -evalue 0.00001 -max_target_seqs 5 -num_threads 4

Also, is there a way to run one vs all of my proteomes blast and not one vs one proteome?

I should add I am super new to local blast and using any kind of coding.