Peace be upon all of you,

Actually I have many questions:

- why in sequence alignment are gaps expressed in a negative scores?

- How can we count the number of possible alignments between two sequences using either Smith-Waterman algorithm or Needleman-Wunsch algorithm with linear gap penalty?

one last request I need to understand how can I do the calculations of Hidden Markov Model in a simplified way as I have a biological background (sorry for saying that but I hate math), may any one help me?

with regards