seems that lookahead grep is the slightly faster solution ... here is the test script I used: 
#!/usr/bin/perl -w
# usage : ./this_script.pl < input_file > captured_benchmarks
use strict;
use Benchmark;
my @data=<>;
my (@res1,@res2,@res3);
timethese (100000000,
    { grep_and => q{
    @res1 = grep /GGGGGACACCTTCTCTCTCT/ && /RH_MEa0001bG06/, @data;
    },
    double_grep => q{
    @res2 = grep /GGGGGACACCTTCTCTCTCT/,grep /RH_MEa0001bG06/,@data;
    },
    lookahead_grep => q{
    @res3 = grep /^(?=.*GGGGGACACCTTCTCTCTCT)(?=.*RH_MEa0001bG06)/,@da
+ta;
    }
}
);

[download]
... and the results 
Benchmark: timing 100000000 iterations of double_grep, grep_and, looka
+head_grep...

double_grep    :
27 wallclock secs (26.98 usr +  0.00 sys = 26.98 CPU) @ 3705899.79/s (
+n=100000000)

grep_and    :
24 wallclock secs (23.05 usr +  0.00 sys = 23.05 CPU) @ 4338959.52/s (
+n=100000000)

lookahead_grep    :
24 wallclock secs (22.83 usr +  0.00 sys = 22.83 CPU) @ 4380585.25/s (
+n=100000000)

[download]

In reply to Re^2: grep for lines containg two variables by l3v3l
in thread grep for lines containg two variables by smoss74

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