Sequence file (@array1) looks like this:

>gi|13470331|ref|NP_101896.1| hypothetical protein 
MFWVTKKALMPFLMLPAGIIFVSAVGYAINWLFSTLFQFQPPLVEGPAGPVTVLIFTITMLLAYDISYYL
>gi|13470319|ref|NP_101897.1| hypothetical protein 
MGAYCQAHPACKVTDRTVIGRRDAAMNAPFVLAIPRTRTFEVVTSAARLAEIAPAWTALWQRAGGLVFQH

my @array2 = qq(13470319 13470331 15460001 13490216);

foreach my $line (@array1)   {
     if ($line =~  /^gi\|(\d+)/)  {
         for (my $i=0;$i<@array2; $i++)  {
               if ($array2[$i] == $1)  {
                  print "$line ";
              }
         }
     }
}