bandedChainAlignment

Function

Calculates a banded alignment around a chain of seeds.

bandedChainAlignment(seedChain, k, alignment, scoreMatrix);

Include Headers

seqan/seeds.h

Parameters

seedChain	A chain of seeds.
k	Half of the width of the band.
alignment	The alignment where the result is stored. Types: Align
scoreMatrix	The score matrix. Types: Simple Score Remarks: Depending on the score matrix the Needleman-Wunsch or the Gotoh algorithm is used. For a description of the algorithm see the masters thesis of C. Kemena, Section 5.3.3 LAGAN Alignment.

Return Values

The score of the alignment.

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