[Seqan-dev] Disallowing gaps in an alignment

[Karrde <karrde.dev@gmail.com>]

Hello, 

I want to perform an alignment such that there are no gaps allowed using the Blosum62 mutation matrix. In practice, one of my sequences will be much smaller than the other. I want it to align as close as possible to the longer sequence without allowing any gaps. Is there a flag or something I can set to disallow any gaps or set the maximum number of gaps allowed?

I'm new to SeQan, but here's what I have so far (test data):

typedef seqan::String<char> TSequence;

typedef seqan::Align<TSequence,seqan::ArrayGaps> TAlign;

TSequence seq1 = "CDFGAAAHC";

TSequence seq2 = "CDEFGAHC";

TAlign align;

resize(rows(align), 2);

assignSource(row(align,0),seq1);

assignSource(row(align,1),seq2);

double score = globalAlignment(align, seqan::Score<int, seqan::ScoreMatrix<seqan::AminoAcid, seqan::Blosum62_>>());

std::cout << "Score: " << score << ::std::endl;

std::cout << align << ::std::endl;

Thanks for any and all help!