Definition of the spliced alignment problem

We start with the formal definitions and statement of the spliced alignment problem.

• Let be a string of letters and let $B=g_i\ldots g_j$ and $B'=g_{i'}\ldots g_{j'}$ be substrings of G. We write B < B' if j<i', i.e. if B ends before B' begins.
• A sequence $\Gamma=\{B_1,\ldots ,B_k\}$ of substrings of G is a chain if $B_1<B_2<B_3<\ldots <B_k$.
• Let $B_1\ast B_2$ denote the concatenation of B₁ and B₂. We denote the concatenation of all the strings from $\Gamma$ by $\Gamma ^{*}$.
• Given two strings G and T, let S(G,T) be the score of the optimal global alignment between them.