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

[Birte Kehr <birte.kehr@fu-berlin.de>]

Hi, is the following one possibility of what you want your alignment to look like?

        ----CDFH--------

             |         

        CAAAADAAAAFAAAAH

Then you should try passing AlignConfig<false, true, true, false>() as an additional parameter to the globalAlignment function. This will not add gap penalties for leading and trailing gaps in the first sequence.

http://docs.seqan.de/seqan/dev3/?p=AlignConfig

http://docs.seqan.de/seqan/dev3/?p=globalAlignment

Birte

Am 23.01.2014 08:19, schrieb Karrde:

Sorry if you got this twice, I just realized I accidentally hit reply instead of reply-all.

First off, thanks for the response.

I tried your idea but I'm not getting the correct results, I still see several gaps in the alignment. I also tried setting the gap-extend to a high cost while leaving gap-open at 0, but this doesn't actually seem to do anything to the score returned.

Here's the code I used:

TSequence seq1 = "CDFH";

TSequence seq2 = "CAAAADAAAAFAAAAH";

TAlign align;

resize(rows(align), 2);

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

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

//trying to set the gap penalty extra high

seqan::Score<int, seqan::ScoreMatrix<seqan::AminoAcid, seqan::Blosum62_>> scoreRoutine(-100,0);

Output from scoreRoutine(-100,0)

Score: 27

      0     .    :    .  

        C----D----F----H

        |    |    |    |

        CAAAADAAAAFAAAAH

Output from scoreRoutine(-100,-100)

Score: -1173

      0     .    :    .  

        C----D----F----H

        |    |    |    |

        CAAAADAAAAFAAAAH

On Jan 23, 2014, at 1:10 AM, Holtgrewe, Manuel <manuel.holtgrewe@fu-berlin.de> wrote:

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

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

*m

________________________________
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!

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

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

*m

---

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!

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