Spec ProfileSeq Score
Score for sequence-to-profile alignments.

Extends Score
All Extended Score
Defined in <seqan/align_profile.h>
Signature template <typename TValue> class Score<TValue, ProfileSeqScore>;

Template Parameters

TValue The integer type to use for representing scores.

Member Function Overview

Interface Function Overview

Interface Functions Inherited From Score

Interface Metafunction Overview

Interface Metafunctions Inherited From Score

Detailed Description

Using this class, you can align sequences to profiles. The profile is assumed to be in the horizontal direction (first row), the sequence in the vertical direction (second row).

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.

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.

#include <iostream>
#include <seqan/align_profile.h>

using namespace seqan;

int main()
{
    typedef ProfileChar<Dna, int> TDnaProfile;
    typedef String<TDnaProfile> TProfileString;

    TProfileString profile = "CGAT";
    DnaString seq = "CGGAAT";

    Gaps<TProfileString> gapsH(profile);
    Gaps<DnaString> gapsV(seq);

    Score<int, ProfileSeqScore> sScheme(profile);

    int val = globalAlignment(gapsH, gapsV, sScheme, NeedlemanWunsch());
    std::cout << "score value = " << val << "\n";

    std::cout << "gaps in profile/sequence\n"
              << "pos\tG\tS\n";
    for (unsigned i = 0; i < length(gapsH); ++i)
        std::cerr << i << "\t" << isGap(gapsH, i) << "\t" << isGap(gapsV, i) << "\n";

    return 0;
}

The output is as follows:

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

Member Functions Detail

Score::Score(); Score::Score(profile);

Constructor

Parameters

profile The profile to copy from (AllocString of ProfileChar objects).

When providing profile, the function assignProfile is automatically used to assign the profile to this class.

Interface Functions Detail

void assignProfile(score, profile);

Assign profile to ProfileSeqScore.

Parameters

score The ProfileSeqScore object to assign the profile for.
profile The profile to assign to the score. AllocString of ProfileChar.