Your problem is that each fasta sequence spans multiple lines. Knowing that the fasta header is ">" you can use that to your advantage by telling your program to split around the fasta separator and slurp all that is in between. Another neater solution is achievable through Bio::SeqIO which requires BioPerl installation on your system. So for the first case, slurping each fasta record the following code gets you there with few modifications, improtantly, note the default separator variable $/was locally modified to ">"

use strict;
use warnings;
use Data::Dumper;

local $/=">";
while(my $fasta_record=<DATA>){
    chomp $fasta_record;
    $fasta_record =~ s/(^>*.+\n)/$1: /;  #add a space after the fasta 
+header 
    $fasta_record =~ s/\n//g;  # remove endlines
    print $fasta_record,"\n";
    }

__DATA__
>protein1
WWWWTCTG
TTWTTTCT
TTWWWC
>protein2
WWWWTCTG
TTWWWC
TTWTTTCT
>protein3
TTWWWC
WWWWTCTG
TTWTTTCT
[download]

I prefer using a BioPerl module to do this kind of tasks since I can get more time to focus on the more important stuff of doing something or the other with the sequences rather than grapple with how to read them in

Assuming that your sequences are in a fasta file called database_filename.fa

use strict;
use warnings;
use Bio::SeqIO;

#initialize a bioperl object instance
my $in = Bio::SeqIO->new(-file=> "database_filename.fa", -format=>"fas
+ta"); 
while(my $seq = $in->next_seq){    #read the sequences in the bioperl 
+object
    print $seq->id," ",$seq->seq; #output,ID space-separated from sequ
+ences 
    print "\n";
    }
[download]

Many thanks bioisham for kindly replying to my post. I will indeed install BioPerl. Hope it will make things smother. Regards, B

Bijgom: Please see How do I post a question effectively?, Writeup Formatting Tips, Markup in the Monastery, What shortcuts can I use for linking to other information? and Perl Monks Approved HTML tags.

---

Give a man a fish:  <%-(-(-(-<

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
[download]

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;
[download]

kroach: I appreciate you're trying to be helpful, but I think it would have been better if Bijgom had re-formatted the OP him- or herself.

---

Give a man a fish:  <%-(-(-(-<

Sorry guys for my mistake...And many thanks Kroach for editing my post...