Class Specialization
ProfileSeq Score
Score for profile-to-sequence alignments.
Using this Score specialization, you can use profiles for the horizontal and sequences for the vertical sequence in the pairwise DP alignment functions.
Scoring works as follows. The integer SEQAN_CONSENSUS_UNITY and fractions thereof are used to express scores. Gap opens in the profile are scored proportional to the number of gaps in the profile with two times unity, gap extends with one times unity at the position. Gap opens in the sequence are scored with two times unity, gap extends in the sequence with unity. Alignments of profile characters to sequence characters are scored with the fraction of profile characters that match the sequence characters times unity.

Score

ProfileSeq Score

class Score<TValue, ProfileSeqScore>;
Include Headers
seqan/align_profile.h
Parameters

TValue | The integer type to use for representing scores.

Specialization of
Score
Metafunctions

DefaultFindBeginPatternSpec | Type of the default findBegin pattern specialization, given a score. (Score)
SequenceEntryForScore | Returns representation type for a character of a position in a sequence. (Score)
Value | Type of the items in the container or behind an iterator. (Score)

Member Functions

Score | Constructor (Score)

Functions

alignmentEvaluation | Given a multiple alignment, this function calculates all kinds of alignment statistics. (Score)
assignProfile | Assign profile to ProfileSeg Score.
bandedChainAlignment | Computes the best global pairwise alignment between two sequences given a non-empty seed chain. (Score)
buildAlignmentGraph | Builds an Alignment Graph from a set of input alignments. (Score)
globalAlignment | Computes the best global pairwise alignment. (Score)
globalAlignmentScore | Computes the best global pairwise alignment score. (Score)
globalMsaAlignment | Computes a global multiple alignment. (Score)
localAlignment | Computes the best pairwise local alignment using the Smith-Waterman algorithm. (Score)
matchRefinement | 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)
score | Returns the score for aligning the entries entryH and entryV. (Score)
scoreGap | Score for gaps. (Score)
scoreGapExtend | Score for extending gaps. (Score)
scoreGapExtendHorizontal | Returns the score for extending a gap in horizontal direction. (Score)
scoreGapExtendVertical | Returns the score for extending a gap in vertical direction. (Score)
scoreGapHorizontal | Returns the score for a gap in horizontal direction. (Score)
scoreGapOpen | Score for opening a gap. (Score)
scoreGapOpenHorizontal | Returns the score for opening a gap in horizontal direction. (Score)
scoreGapOpenVertical | Returns the score for opening a gap in vertical direction. (Score)
scoreGapVertical | Returns the score for a gap in vertical direction. (Score)
scoreMatch | Match score. (Score)
scoreMismatch | Mismatch score. (Score)
sequenceEntryForScore | Helper function for element access, depending on score type. (Score)
setScoreGap | Set gap opening and extension score. (Score)
setScoreGapExtend | Set gap extension score. (Score)
setScoreGapOpen | Set gap opening score. (Score)
setScoreMatch | Set match score. (Score)
setScoreMismatch | Set mismatch score. (Score)
splitAlignment | Compute split alignments. (Score)
sumOfPairsScore | Given a multiple alignment, this function calculates the sum-of-pairs score. (Score)

Examples
The following example uses the ProfileSeq Score to align a sequence against a profile. Note that we print the gap state for each position since profiles cannot be printed to one stdout character.
File "profile_seq_score.cpp"

1 | #include <iostream>
2 | #include <seqan/align_profile.h>
3 |
4 | int main()
5 | {
6 | typedef seqan::ProfileChar<seqan::Dna, int> TDnaProfile;
7 | typedef seqan::String<TDnaProfile> TProfileString;
8 |
9 | TProfileString profile = "CGAT";
10 | seqan::DnaString seq = "CGGAAT";
11 |
12 | seqan::Gaps<TProfileString> gapsH(profile);
13 | seqan::Gaps<seqan::DnaString> gapsV(seq);
14 |
15 | seqan::Score<int, seqan::ProfileSeqScore> sScheme(profile);
16 |
17 | int val = globalAlignment(gapsH, gapsV, sScheme, seqan::NeedlemanWunsch());
18 | std::cout << "score value = " << val << "\n";
19 |
20 | std::cout << "gaps in profile/sequence\n"
21 | << "pos\tG\tS\n";
22 | for (unsigned i = 0; i < length(gapsH); ++i)
23 | std::cerr << i << "\t" << isGap(gapsH, i) << "\t" << isGap(gapsV, i) << "\n";
24 |
25 | return 0;
26 | }

score value = -2097152
gaps in profile/sequence
pos G S
0 0 0
1 1 0
2 0 0
3 1 0
4 0 0
5 0 0
Example Programs
Local Alignments, Global Alignments
SeqAn - Sequence Analysis Library - www.seqan.de

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