Class Specialization
Score ChainSoP
Scoring scheme for chaining that uses a special method for scoring the gaps between two fragments.
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Score ChainSoP | |||||||
Parameters
Type of the score values. |
Remarks
This scoring scheme is used to score gaps between to fragments in chaining.
Specialization of
Metafunctions
| Type of the default findBegin pattern specialization, given a score. (Score) | |
| Type of the items in the container or behind an iterator. (Score) |
Functions
| Given a multiple alignment, this function calculates all kinds of alignment statistics. (Score) | |
| Builds an Alignment Graph from a set of input alignments. (Score) | |
| Computes the best global pairwise alignment. (Score) | |
| Computes the best global pairwise alignment score. (Score) | |
| Computes a global multiple alignment. (Score) | |
| Computes the best pairwise local alignment using the Smith-Waterman algorithm. (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. (Score) | |
| Returns the score for aligning the characters | |
| Score for gaps. (Score) | |
| Score for extending gaps. (Score) | |
| Score for opening a gap. (Score) | |
| Match score. (Score) | |
| Mismatch score. (Score) | |
| Set gap opening and extension score. (Score) | |
| Set gap extension score. (Score) | |
| Set gap opening score. (Score) | |
| Set match score. (Score) | |
| Set mismatch score. (Score) | |
| Given a multiple alignment, this function calculates the sum-of-pairs score. (Score) |
Example Programs
SeqAn - Sequence Analysis Library - www.seqan.de