use strict;
print scalar <DATA>;    # print first #PLOT1

while (<DATA>) {
    chomp;              # get rid of EOL
    print /#PLOT/ ? "\n$_\n" : "$_ ";
} ## end while (<DATA>)

__DATA__
#PLOT1
a b c d f g i
a c g s h
b h f d
#PLOT2
b g d i s e
w d u
b a o
n i o p w q c u s t r r y
#PLOT3
e r t d v g
v g b
[download]

#PLOT1
a b c d f g i a c g s h b h f d 
#PLOT2
b g d i s e w d u b a o n i o p w q c u s t r r y 
#PLOT3
e r t d v g v g b
[download]

Whether it is better (for whatever definition of better) I do not know. My solution uses very little memory as it never holds more than one line in memory, whereas a foreach based solution will (usually) hold all the data in memory at once. Of course for such a small sample of data it does not matter.

This would be a better question if:

1. You showed us what you want
2. You showed us what you've tried, and where you're stuck

For 1, either a sample of your desired output using the data supplied, or a clear(er) explanation of your intent, or, better yet, both.

While, re 2, the Monks give generously of their time and wisdom to those who show effort, but tend to frown disapprovingly on those who see the Monastery as a 'free coding machine'

I suggest using a mixture of a while loop, perhaps a join statement, and a dash of split. However, you have not really provided much information so my suggestion could be entirely wrong.

the program i have written is

open(FH,"input.txt") or die "cant open";
@array=<FH>;
foreach(@array){
if($_!=~m/^>/)
{
$_=~s/\n//g;
print "$_\n";
}
}
[download]

the desired result is

#PLOT1
a b c d f g i a c g s h b h f d 
#PLOT2
b g d i s e w d u b a o n i o p w q c u s t r r y
#PLOT3
e r t d v g v g b
[download]

$count = 0;
while (<FILE>)
{
    if ($_ =~ /^\#/) {
        $count ++;
        $temp{$count} = "";
    }
    else{
        chomp ();
        $temp{$count} .=  " ".$_;
    }
}
for $i (0 .. $count) {
print $temp{$i} ."\n";
}
[download]

using perl how do i place all the alphabets in a single line after each plot? is 'while' loop better or 'for' loop?

What code do you have so far? Is that your input or the desired output?

the program i have written is

open(FH,"input.txt") or die "cant open";
@array=<FH>;
foreach(@array){
if($_!=~m/^>/)
{
$_=~s/\n//g;
print "$_\n";
}
}

the desired result is

#PLOT1
a b c d f g i a c g s h b h f d 
#PLOT2
b g d i s e w d u b a o n i o p w q c u s t r r y
#PLOT3
e r t d v g v g b
[download]

if($_!=~m/^>/)
[download]

I don't see any ">" characters in your input. What do you expect the line above to do (also, the "not matches" operator is "!~", not "!=~")?