[EMBOSS] Match mass sequences for mass sequences

[JEEYOUNG LEE]

Dear Sir

I'm sorry for a perhaps naive question.
I want to align sequences of 1000 pairs. For example, "A" file
includes 1000 sequences and "B" file includes 1000 sequences and two
file will be compared. I'd like to find certain sequence( X gene) of A
file which have high sequence similarity with some sequence ( X' gene)
in B file. Then, certain gene (Y) in "A" file will be matched with Y'
gene which have high identity in B file. Finally, I want to get
matched 1000 pairs and their identity score.  At one time, can I match
mass sequences using Jemboss? How can I handle this problem?

Sincerely,

Lee, Jee Young