Re: [Seqan-dev] Disallowing gaps in an alignment
- From: Karrde <karrde.dev@gmail.com>
- To: "Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>
- Date: Thu, 23 Jan 2014 00:19:25 -0800 (PST)
- Cc: SeqAn Development <seqan-dev@lists.fu-berlin.de>
- Reply-to: SeqAn Development <seqan-dev@lists.fu-berlin.de>
- Subject: Re: [Seqan-dev] Disallowing gaps in an alignment
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 alignmentHello,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.*mFrom: 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 alignmentHello,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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- [Seqan-dev] Disallowing gaps in an alignment
- From: Karrde <karrde.dev@gmail.com>
- Re: [Seqan-dev] Disallowing gaps in an alignment
- From: "Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>
- [Seqan-dev] Disallowing gaps in an alignment
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