Class Specialization
Simple Score
Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.
Simple Score |
Include Headers
seqan/score.h
Parameters
The value type. Default: int |
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
Adds a seed to an existing SeedSet using different algorithms for local chaining. | |
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) | |
Extends a seed. | |
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 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 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) |
Shortcuts
Simple scoring scheme. |
Example Programs
See Also
SeqAn - Sequence Analysis Library - www.seqan.de