If you really want to prompt for input from the user after the program starts, then the advice in the first reply will take care of the immediate problem. But I would recommend using a command-line argument, which your script sees as $ARGV[0] (you run your script via a command-line shell, don't you?)

Apart from that, you'll be better off using a placeholder in the sql query string, and passing the value to search for as a parameter when you execute the query:

#!/usr/bin/perl

use strict;  # don't comment this out, and don't capitalize it.
use DBI;

my $Strain;

if ( @ARGV ) {
    $Strain = shift;  # get your target string from the command line
}
else {
    print "Please Enter the Strain Name: ";
    $Strain = <>;
    chomp $Strain;
}

$dbh = DBI->connect('dbi:mysql:sampledb','root','******')
    or die "Connection Error: $DBI::errstr\n";

$sql = <<EOS;  # let's make it easier to read while we're at it
SELECT
 feature.fastaId,
 feature.contigId,
 feature.orfId,
 strain.strainName,
 sequence.ntseq, sequence.aaseq
from feature
  left join strain on feature.id=strain.id
  left join sequence on feature.id=sequence.id
where strainName = ?
EOS

$sth = $dbh->prepare($sql);
$sth->execute( $Strain )
    or die "SQL Error: $DBI::errstr\n";

while (@row = $sth->fetchrow_array) {
    print "@row\n";
}
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