[BiO BB] RE: Some questions of alignment (Evgeny Cheremushkin)

Zhang, Yuanji yjzhang at noble.org
Fri Jul 9 13:11:21 EDT 2004

Dear Evgeny,

Last time we talked about alignment of length L given M mispairs. The total
possible alignments are C(L, M).

Now I am trying to formalize the second question of number of alignments
undetectable by blastn with word size = 7 nt. Suppose '0' represents
identity, and '1' for one mismatch (total mismatches = M). How many
alignments do not have >=7 continuous '0's? Here is an example
:000000010000100001000000 (detectable. L = 24, M = 3) and
100000010000100001000000 (undetectable, no 7 or more '0's in a row).

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