Class Specialization
Simple Score
Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.
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Simple Score | |||||||
Parameters
The value type. Default: int |
Specialization of
Functions
| Given a multiple alignment, this function calculates all kinds of alignment statistics. (Score) | |
| Calculates a banded alignment around a Seed. | |
| Calculates a banded alignment around a chain of seeds. | |
| Extends a seed. | |
| Extenstion of seeds. | |
| Constructs a alignment from a ChainedSeed. | |
| Computes the best global alignment of the two sequences. (Score) | |
| Computes the best local alignment of two sequences. (Score) | |
| Refines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the segments partly overlap. They are either identical (fully overlapping) or non-overlapping. Refines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the segments partly overlap. They are either identical (fully overlapping) or non-overlapping. (Score) | |
| Computes multiple local alignments of two sequences. (Score) | |
| The score for aligning two values according to a scoring scheme. (Score) | |
| Score for gaps. | |
| Score for extending gaps. | |
| Score for opening a gap. | |
| Match score. | |
| Mismatch score. | |
| Calculates the score of a seed. | |
| Computes the best local alignment of the (two) sequences given in align. (Score) | |
| Computes next best local alignment. (Score) | |
| Given a multiple alignment, this function calculates the sum-of-pairs score. (Score) |
Shortcuts
| Simple scoring scheme. |
Example Programs
See Also
SeqAn - Sequence Analysis Library - www.seqan.de