Bl2Seq With Multi Fasta

Hello,

I have two groups of sequences in separate files (1.fasta and 2.fasta). I need to make comparison between them. However I cannot run

bl2seq -i 1.fa -j 2.fa -p blastp -o output

because bl2seq is expecting only one sequence in a fasta file.

Is splitting multi fasta files the only option to compare each sequence in 1.fa with each sequence in 2.fa?

Thanks for help