hii..thanks for your reply..the prob is that there can be more or less lines after both >first and >firsta. No fixed number of lines or strings...

>firsta is going to have lesser number of molecules than >first as there is unmatched portion in >firsta

But >fist and >firsta have same number of lines..

for eg..If no. of lines for >first is 8, then it is same for >firsta

Seems like I am totally lost in regex of Perl...studying for last few days n I am frustrated now :(

any suggestion?