Thanks for your replies.I did get the two output files now ,one having the headers and associated protein sequences and the other with headers of Sec structures and associated structures.

       
if ($_ =~ /sequence/){
        @headerseq = split('\n',$_);
        print OFILE1 "@headerseq\n";
        }
        elsif ($_ =~ /^(\w*)$/){
        @sequence = $_;
        print OFILE1 "@sequence\n";
        }
        elsif ($_ =~ /secstr/) {
        @headersec = split('\n',$_);
        print OFILE2 "@headersec\n";
        }
        else {
        @secseq = $_;
        print OFILE2 "@secseq\n";
        }
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