Thanks for the good question and the right answers given so far. As far as I am concern, I have really learned a lot from the post. one thing that is missing so far is that both must be power of two. That is , 2^(x). The higher the sequence length, the more data to work on, and the better the result you get, though at the expense of your system memory as said in some posts.
Although, one thing that is yet to be cleared to me is that, if the memory of my system is higher than that of the others, I will definitely get better results base on my ability to increase my sequence length. Then, whose system (the one with higher or lower memory) can we use to predict a real experimental implementation or are these parameters (sequence length, etc) equally adjustable in the experiment?. Thanks alot