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

##</code><code>##

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

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

##</code><code>##