[BiO BB] Some questions of alignment

[Zhang, Yuanji]

Hello Dear Colleagues,

I have 2 mathmatical questions about necleotide sequence alignment:

1. Given 2 homologous sequences of the same length (L) (e.g., L = 30 nt),
and mismatches (M, 0 <= M <= L) are allowed in the alignment, how many
possible alignments will be? (One assumption: biologically it does not make
much sense when M = L, but mathmatically, there is one possible alignment
between the 2 sequences, and mismatch occurs in every position.) 

2. Suppose blastn is used to detect the alignment. Given word size = 7,
mismatch punishment = -1, and match reward = 1, how many alignments cannot
be detected by blast?

Any idea is welcome.