Pairwise alignment with infinite gapExtension
I can't understand how the +/- Inf gapExtension option works for global alignment scoring. Even when testing with -Inf gapExtension and identical strings, "yy", I get a score of -Inf and optimal alignment, "y- / -y". I can't find out why the result is this.
Wouldn't the matrix be the following (match: +1, gap: -10, gapExtension; -Inf)? Could anyone please help?
_____x______y______y
x____0_____-Inf____-Inf
y___-Inf_____1_____-Inf
y___-Inf____-Inf______2
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h3668025 •
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