i have written a program to save each and every line in a seperate array. this is the program

which does not meet it's purpose, since you are saving all lines of your data file which don't begin with either ENTRY, TITLE, ORGANISM or ACCESSIONS into a single array which you name @se.

Let's look at your data file. It seems to be composed of multi-line records, in which each field begins on a separate line. Each field has an identifier up front (except the last record field which is just a sequence of chars with no blank in it), and some fields appear to be multi-line as well.

Since there is no record separator, you can only tell that all fields of a record are read when all field contents are read. Since your records appear to be ordered, I assume that is the case when that single-word line appears. All fields are stored in an anonymous array, which is pushed onto an array when done reading. After storing each record, a new anonymous array is initialized for the next record:

my $file = '/home/guest/sampir.txt');
open (PIR, '<', $file) or die "Can't read '$file': $!\n";
my @arr = ();
my $se = [];             # anonymous record array
while(<PIR>)
{
    chomp;
    if (/^(\w+)\s+/)     # new field identifier, followed by blanks
    {
        push @$se, $_; 
    }
    elsif (s/^\s+/ /)    # if we can strip leading blanks,
                         # it's a continuation line
    {
        $se->[-1] .= $_; # append to last field of this record
    }
    elsif(/^\w+$/)       # must be the last field of the record
    {
        push @$se, $_;   # save the last field
        push @arr, $se;  # save the record array reference
        $se = [];        # and make a new array reference for the next
+ record
    }
    else
    {
        die "Unknown line type at line $. of '$file'\n";
    }
}
[download]

Now you have all records in an array of arrays. See perldsc.

@arr = (
  [
    'ENTRY            CCHU       #type complete',
    'TITLE            cytochrome c [validated] - human Homo sapiens',
    'ORGANISM         #formal_name Homo sapiens #common_name man',
    'ACCESSIONS       A31764; A05676; I55192; A00001',
    'MGDVEKGKKIFIMKCSQCHTVEMGDVEKGGKHKTGPNLHGMIYARAJLFGRKTSEKGQAPGYSYT
+AANKNKGIIWGEDTLMEYLENPKKYIP'
  ],
  [
    'ENTRY            CCCZ       #type complete',
    'TITLE            cytochrome c - chimpanzee (tentative sequence)',
    'ORGANISM         #formal_name Pan troglodytes #common_name chimpa
+nzee',
    'ACCESSIONS       A00002',
    'GDVEKGKKIFIMKCSQCHTSEKVEKGSSSKHKSSSTGPNLHGLMIYARAJFGRKTGSEKQAPGYS
+YTAANKNKGIIWGED'
  ],
  [
    'ENTRY            CCMQR      #type complete',
    'TITLE            cytochrome c - rhesus macaque (tentative sequenc
+e) Macaca mulatta ',
    'ORGANISM         #formal_name Macaca mulatta #common_name rhesus 
+macaque',
    'ACCESSIONS       A00003',
    'GDVEKGKKIFIMKCSQSEKCHTVEKGGSSSSKHKTGPNLHGSSEKEMIYARAJKSEKLFGAAAAA
+AAARKTGQAPGYSYTAANKSSSSNKGITWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEE'
  ],
  [
    'ENTRY            CCMKP      #type complete',
    'TITLE            cytochrome c - spider monkey',
    'ORGANISM         #formal_name Ateles sp. #common_name spider monk
+ey',
    'ACCESSIONS       A00004',
    'GDVFKGKRIFIMKCSQCHTVESSSSKGGKHKTGPNLHGLMIYARAJSEKFGSSSSSSSSSSR'
  ]
);
[download]

print $arr[0]->[1],"\n";
[download]

TITLE            cytochrome c [validated] - human Homo sapiens
[download]

--shmem

_($_=" "x(1<<5)."?\n".q·/)Oo.  G°\        /
                              /\_¯/(q    /
----------------------------  \__(m.====·.(_("always off the crowd"))."·
");sub _{s./.($e="'Itrs `mnsgdq Gdbj O`qkdq")=~y/"-y/#-z/;$e.e && print}