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.