Re: [Seqan-dev] Disallowing gaps in an alignment

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

Hi, simply use very high gap costs in the constructor.

http://docs.seqan.de/seqan/dev3/?p=MatrixScore#Score

*m

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From: Karrde [karrde.dev@gmail.com]
Sent: Wednesday, January 22, 2014 11:48 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] Disallowing gaps in an alignment

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!