We start with the formal definitions and statement of
the spliced alignment problem. Let
be a
string of letters and let
and
be substrings of G.
We write B < B' if j<i', i.e.
if B ends before B' begins. A sequence
of substrings of G is a chain if
.
We denote the concatenation of all the
strings from
by
.
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
.
A target sequence (related protein)
.
A set
of blocks (substring of G).
Question: Find a chain
of blocks from B such that
is maximum.