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 characters | |
Score for gaps. (Score) | |
Score for extending gaps. (Score) | |
Returns the score for extending a horizontal gap after | |
Returns the score for extending a vertical gap after | |
Returns the score for a horizontal gap after | |
Score for opening a gap. (Score) | |
Returns the score for opening a horizontal gap after | |
Returns the score for opening a vertical gap after | |
Returns the score for a vertical gap after | |
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