extendSeed

Function

extendSeed

Extends a seed.

void extendSeed(seed, database, query, direction, MatchExtend);

void extendSeed(seed, database, query, direction, scoreMatrix, scoreDropOff, {UngappedXDrop, GappedXDrop});

Include Headers

seqan/seeds.h

Parameters

seed	The seed to extend. Types: Seed
query	The query sequence (vertical). Types: String
database	The database sequence (horizontal). Types: String
direction	Defines the direction in which the seed should be extended. Types: Extension Direction
scoreDropOff	The score drop after which the extension should stop. The extension stops if this value is exceeded. Remarks: Only used for the algorithms UngappedXDrop and GappedXDrop
scoreMatrix	The scoring scheme. Types: Simple Score Remarks: Only used for the algorithms UngappedXDrop and GappedXDrop

Remarks

You can use the tags, MatchExtend, UngappedXDrop, and GappedXDrop.

Note that the diagonals updated in seed do not necessarily reflect the diagonals for the optimal extension but the diagonals used in all traces of the extension. However, they are guaranteed to include the optimal extension's trace.

Member of

Seed

Examples

The documentation of the class Seed contains an example for seed extension.