Aaah, quite right. I am curious about the line endingness of FILE then (in which case, chomp would not do the right thing either :-/ )

The input data is like

>1elwA
AAAAAASSSSSSSSSSSSSSDDDDDDDDDDDFFFFFFFFFF
>1flwA
GGGGGGGGGGHHHHHHHHHHHHIIIIIIIIIIIIIIJJJJJJJJJJ
>1ghwA
KKKKKKKKKKLLLLLLLLLLMMMMMMMMMMNNNNNNNNNNOOOOO
[download]

Where >1elwA, >1flwA, >1ghwA should be the keys of the hashes and the respective data should be the value of the hash. The code/sub for storing in the file is

#!/usr/bin/perl

my %seqInfo = ();

open(FILE, 'test.fasta');
{
while(<FILE>)
{
my $line = $_;
 if ($line =~ />.*/)
  {
  #print "$&\n";
  }
else
  {
  #print "$line\n";
  }
$seqInfo{$&} = $line;
print "$& => $line\n";
}
}
[download]

and the output is

=> >1elwA

 => AAAAAASSSSSSSSSSSSSSDDDDDDDDDDDFFFFFFFFFF

 => >1flwA

 => GGGGGGGGGGHHHHHHHHHHHHIIIIIIIIIIIIIIJJJJJJJJJJ

 => >1ghwA

 => KKKKKKKKKKLLLLLLLLLLMMMMMMMMMMNNNNNNNNNNOOOOO
[download]

However according to my understanding the output should be like

>1elwA => AAAAAASSSSSSSSSSSSSSDDDDDDDDDDDFFFFFFFFFF
[download]

Maybe the file is not properly stored as keys and values :( :(

Thankyou for the replies, Infact I have figured out the problem and have solved it. I have added a counter in it and its working fine + I have replaced the $& character with the similar substr expression as advised. So now the code is working fine. Thanks again for all the replies... :) :) :)