That may work in this case, assuming the genes are all the same length. But it would also match if a line from file1 appeared a a substring of a line in file2, so a more general non-perl solution to "I want the lines two files have in common" is to use comm. My guess is that using comm on two sorted files is probably less resource-intensive than asking grep to turn an entire file into search strings, too. 

sort file1 >file1.sorted
sort file2 >file2.sorted
comm -12 file1.sorted file2.sorted >common.lines

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Aaron B.
My Woefully Neglected Blog, where I occasionally mention Perl.

In reply to Re^2: Common between two lists by aaron_baugher
in thread Common between two lists by perllearner007

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