Hi serafinososi,

...If the line starts with “>” (it is the first line of a FASTA file) the line is not considered...

What if the line that starts with ">" is more than one in the file what happens?

If I understand the OP's question, using the data provided, if I may suggest (adding to what others have said) using perl function split may do like so:

use warnings;
use strict;

my $protein;

while (<DATA>) {
    if (/^>/) {
        next;
    }
    else {
        $protein = join '', split;
    }
}

my $number_of_F = grep { /F/ } split //, $protein;

print "The aminoacid sequence: ", $protein, " contains ", $number_of_F
+,
  " Phenylalanine aminoacids", $/;

__DATA__
>gi|403369491|gb|EJY84591.1| Transcriptional regulator, Sir2 family pr
+otein Oxytricha trifallax

MMKQLIKHNKNTPLFNFLRVKFSSTAATIQTQQTVNKPIESKFKEEKLDNYHDIYEKSKRLAEQISQSKS
+ FICFTGAGLSTSTGIPDYRSTSNTLAQTGAGAYELEISEEDKKSKTRQIRSQVQRAKPSISHMALHAL
+ME NGYLKHLISQNTDGLHLKSGIPYQNLTELHGNTTVEYCKSCSKIYFRDFRCRSSEDPYHHLTGRQC
+EDLK CGGELADEIVHFGESIPKDKLVEALTAASQSDLCLTMGTSLRVKPANQIPIQTIKNKGQLAIVN
+LQYTPF DEIAQIRMHSFTDQVLEIVCQELNIKIPEYQMKRRIHIIRNAETNEIVVYGSYGNHKNIKLS
+FMQRMEYI DNKNHVYLALDKEPFHIIPDYFNFQNINTDQEEVEFRIHFYGHNSEPYFQLTLPRQSILE
+LQAGEHLICD ITFDYDKLEWK
[download]