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The LogDelLocalRefine Function

The LogDelLocalRefine function is must the same as the LocalAlign routine from the previous section. It finds the best local alignment for a PAM distance but using a logarithmic deletion cost.

Calling Sequences:
LogDelLocalRefine(m, DM)
m : Match
DM : DayMatrix

Returns: Match

Synposis: Via dynamic programming and the Dayhoff matrix DM, LogDelLocalRefine finds the highest scoring local alignment between sequences m1 and m2 contained in the Match structure m.

The similarity scoring in the dynammic programming is done relative to DM, therefore, the PAM distance of the alignment is the PAM distance of DM. The gap scoring function is a logarithmic deletion function.

> DB := ReadDb('Sample/SH2');
> CreateDayMatrices();
> m := Match(op(Sequence(Entry(1))), op(Sequence(Entry(2))));
> align := LogDelLocalRefine(m, DM);
> print(align);

The LogDelLocalRefine routine is slower than LocalRefine due to its use of the logarithmic deletion function. However, this deletion function tends to produce better results especially when attempting to detect longer distance homologies [].

Gaston Gonnet