A more readable version of the question:

Hello Monks, I have a problem and I would greatly appreciate your wisdom to solve it. So, I am reading from a fasta file (containing protein seqeunces) while looping over and trying to print protein sequences.

My problem is: When trying to print each protein sequence that I have in my hash, the sequences are broken down as follows:

Protein sequence:STARTXXXXX
Protein Sequence: XXXXXXXXX
Protein sequence: XXXXXXEND
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Question: How could I avoid this?

Here is my script:

use warnings;
my %database;
my $protein_id       = "";
my $line             = "";
my $datbase_filename = "";
my $start            = ">DDB";
my $end = "";

#input1: open the file containg the protein sequences.
print "Please enter the path to the fasta file of protein sequences\n"
+;
#put the file name into $filenam
$database_filename = <STDIN>;
chomp($database_filename);    #remove newline

#open the file containing protein sequences in fasta format
open(MYFILE1, "<$database_filename")
  or die "Unable to open $database_filename: $!\n";

while (<MYFILE1>) {
    chomp;                    #remove newline
    $line = $_;
    print "Line i: $_\n";     #test
    if (($line =~ m/^>DDB/) and ($line =~ m/to\s\d+$/)) {
        $protein_id = $line;
        print "protein ID: $protein_id\n";    #test
    } else {
        # associating the protein sequence in my %proteins to its ID
        $proteins{$protein_id} = $line;
        print "sequence: $line\n";            #test
    }
}
exit;
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Many thanks in advance.