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Spliced alignment problem

We start with the formal definitions and statement of the spliced alignment problem. Let $G=g_1g_2\ldots g_n$ 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 $B_1<B_2<B_3<\ldots <B_k$. 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.

Problem 7.2   Spliced alignment
Instance: A new genomic sequence $G= g_1\ldots g_n$. A target sequence (related protein) $T=t_1\ldots t_m$. A set $B={B_1,\ldots ,B_k}$ of blocks (substring of G).
Question: Find a chain $\Gamma$ of blocks from B such that $S(\Gamma ^{*},T)$ is maximum.



Itshack Pe`er
1999-02-03