Class Specialization
Score Matrix
A general scoring matrix.
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Score Matrix | |||||||
Include Headers
seqan/score.h
Parameters
Type of the score values. Default: | |
Type of alphabet underlying the matrix. Default: |
Specialization of
Metafunctions
| Type of the default findBegin pattern specialization, given a score. (Score) | |
| Returns representation type for a character of a position in a sequence. (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) | |
| Computes the best global pairwise alignment between two sequences given a non-empty seed chain. (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) | |
| Load a score matrix from a file. | |
| 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 entries | |
| Score for gaps. (Score) | |
| Score for extending gaps. (Score) | |
| Returns the score for extending a gap in horizontal direction. (Score) | |
| Returns the score for extending a gap in vertical direction. (Score) | |
| Returns the score for a gap in horizontal direction. (Score) | |
| Score for opening a gap. (Score) | |
| Returns the score for opening a gap in horizontal direction. (Score) | |
| Returns the score for opening a gap in vertical direction. (Score) | |
| Returns the score for a gap in vertical direction. (Score) | |
| Match score. (Score) | |
| Mismatch score. (Score) | |
| Helper function for element access, depending on score type. (Score) | |
| Set the value of the given matrix to the default value. | |
| Set the substitution score between two values. | |
| 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) | |
| Compute split alignments. (Score) | |
| Given a multiple alignment, this function calculates the sum-of-pairs score. (Score) | |
| Write a score matrix to a stream. |
Shortcuts
| Blosum30 scoring matrix. | |
| Blosum45 scoring matrix. | |
| Blosum62 scoring matrix. | |
| Blosum80 scoring matrix. | |
| Pam120 scoring matrix. | |
| Pam200 scoring matrix. | |
| Pam250 scoring matrix. | |
| Pam40 scoring matrix. | |
| Vtml200 scoring matrix. |
Example Programs
SeqAn - Sequence Analysis Library - www.seqan.de