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
[download]