You seem confused about what your program does, so I thought I'd just tell you.
$inFile = "animals.txt";
open (IN, $inFile) or die "Can't find file: $inFile";
@animallist = (<IN>);
# here you define a file name, open a file, and read all of the lines
# in the file into the array @animallist
foreach $line (@animallist) {
# here you iterate over all the lines, putting each line into $line
if ($line =~ $search) {
print "$line <br> <br>";
}
# here you perform the regex match: $line =~ /$search/ and if it
# succeeds, print $line
}
# here you end the loop
if ($line ne $search) {
print "$search isn't in the animal list";
}
# here you take the now uninitialized variable $line and try to match
# it against the as of yet undefined variable $search
# If both of these variables are undefined, and you are not using warnings
# it will simply return false (because "" ne "" is false)
# without warning about undefined variables in ne
You should be aware that even if your entire line was, for example, cat, you still could not compare it using ne to the string cat, because when read from a file, it has a trailing newline, so it is really cat\n. Unless you chomp it.
It seems redundant to tell you, but of course you cannot check if the file does not contain $search after you finished reading the file. You have to do that while reading the file.