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) | |
| Type of the items in the container. (Score) |
Functions
| Given a multiple alignment, this function calculates all kinds of alignment statistics. (Score) | |
| Computes the best global alignment of the two sequences. (Score) | |
| Computes a global multiple alignment. (Score) | |
| Load a score matrix from a file. | |
| 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. (Score) | |
| Computes multiple local alignments of two sequences. (Score) | |
| Returns the score for aligning the characters | |
| Returns the score for aligning the characters | |
| Set the value of the given matrix to the default value. | |
| Set the substitution score between two values. | |
| Given a multiple alignment, this function calculates the sum-of-pairs score. (Score) |
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
