Re: [Seqan-dev] local alignment with blosum scoring matrix

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

Dear Youngik,

without a working minimal example, we will not be able to help you  
with your code.

There is an example for working with Blosum matrices and global  
alignments in [1] as you probably already know. Maybe you can combine  
it with the local alignment example in [2] to achieve what you need?

Bests,
Manuel

[1] http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/Alignments#MultipleAlignments
[2] http://trac.mi.fu-berlin.de/seqan/browser/trunk/seqan/core/demos/alignment_local.cpp

Am 05.08.2011 um 17:30 schrieb Young-ik Yang:

> Would you let me know which local alignment algorithm support  
> scoring matrix
> such as blosum62?
> If any, can you show me a function call or an example?
>
> I am using seqan 1.3.
> I am attaching error messages from local alignment call at the end  
> of the
> message.
>
> Thanks,
> Youngik.
>
>
> /home/yyang/bin/seqan/seqan/graph_align/ 
> graph_align_smith_waterman.h: In
> function 'typename seqan::Value<TRight, 0>::Type
> seqan::_alignSmithWaterman(TTrace&, const TStringSet&, const  
> TScore&, typename
> seqan::Value<THolder, 0>::Type&, TIndexPair&, TForbidden&) [with  
> TTrace =
> seqan::String<unsigned char, seqan::Alloc<void> >, TStringSet =
> seqan::Align<seqan::String<seqan::SimpleType<unsigned char,  
> seqan::AminoAcid_>,
> seqan::Alloc<void> >, seqan::ArrayGaps>, TScore = seqan::Score<int,
> seqan::ScoreMatrix<seqan::SimpleType<unsigned char,  
> seqan::AminoAcid_>,
> seqan::Blosum62_> >, TIndexPair = size_t [2], TForbidden =  
> seqan::Nothing]':
> /home/yyang/bin/seqan/seqan/graph_align/graph_align_smith_waterman.h: 
> 381:
> instantiated from 'typename seqan::Value<TLeft, 0>::Type
> seqan::_localAlignment(const TStringSet&, const TScore&,  
> seqan::SmithWaterman)
> [with TStringSet =  
> seqan::Align<seqan::String<seqan::SimpleType<unsigned char,
> seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::ArrayGaps>, TScore =
> seqan::Score<int, seqan::ScoreMatrix<seqan::SimpleType<unsigned char,
> seqan::AminoAcid_>, seqan::Blosum62_> >]'
> /home/yyang/bin/seqan/seqan/graph_align/graph_align_interface.h:378:
> instantiated from 'TScoreValue seqan::localAlignment(const  
> TStringSet&, const
> seqan::Score<TScoreValue, TScoreSpec>&, TTag) [with TStringSet =
> seqan::Align<seqan::String<seqan::SimpleType<unsigned char,  
> seqan::AminoAcid_>,
> seqan::Alloc<void> >, seqan::ArrayGaps>, TScoreValue = int, TSpec =
> seqan::ScoreMatrix<seqan::SimpleType<unsigned char,  
> seqan::AminoAcid_>,
> seqan::Blosum62_>, TTag = seqan::Tag<seqan::SmithWaterman_>]'
> alignment_local.cpp:65:   instantiated from here
> /home/yyang/bin/seqan/seqan/graph_align/graph_align_smith_waterman.h: 
> 233: error:
> no match for 'operator[]' in 'str[0]'
> /home/yyang/bin/seqan/seqan/graph_align/graph_align_smith_waterman.h: 
> 234: error:
> no match for 'operator[]' in 'str[1]'
> /home/yyang/bin/seqan/seqan/score/score_base.h: In function 'TValue
> seqan::score(const seqan::Score<TValue, TSpec>&, TPos1, TPos2, const  
> TSeq1&,
> const TSeq2&) [with TValue = int, TSpec =
> seqan::ScoreMatrix<seqan::SimpleType<unsigned char,  
> seqan::AminoAcid_>,
> seqan::Blosum62_>, TPos1 = long unsigned int, TPos2 = long unsigned  
> int, TSeq1 =
> seqan::SimpleType<unsigned char, seqan::AminoAcid_>, TSeq2 =
> seqan::SimpleType<unsigned char, seqan::AminoAcid_>]':
> /home/yyang/bin/seqan/seqan/graph_align/graph_align_smith_waterman.h: 
> 291:
> instantiated from 'typename seqan::Value<TRight, 0>::Type
> seqan::_alignSmithWaterman(TTrace&, const TStringSet&, const  
> TScore&, typename
> seqan::Value<THolder, 0>::Type&, TIndexPair&, TForbidden&) [with  
> TTrace =
> seqan::String<unsigned char, seqan::Alloc<void> >, TStringSet =
> seqan::Align<seqan::String<seqan::SimpleType<unsigned char,  
> seqan::AminoAcid_>,
> seqan::Alloc<void> >, seqan::ArrayGaps>, TScore = seqan::Score<int,
> seqan::ScoreMatrix<seqan::SimpleType<unsigned char,  
> seqan::AminoAcid_>,
> seqan::Blosum62_> >, TIndexPair = size_t [2], TForbidden =  
> seqan::Nothing]'
> /home/yyang/bin/seqan/seqan/graph_align/graph_align_smith_waterman.h: 
> 381:
> instantiated from 'typename seqan::Value<TLeft, 0>::Type
> seqan::_localAlignment(const TStringSet&, const TScore&,  
> seqan::SmithWaterman)
> [with TStringSet =  
> seqan::Align<seqan::String<seqan::SimpleType<unsigned char,
> seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::ArrayGaps>, TScore =
> seqan::Score<int, seqan::ScoreMatrix<seqan::SimpleType<unsigned char,
> seqan::AminoAcid_>, seqan::Blosum62_> >]'
> /home/yyang/bin/seqan/seqan/graph_align/graph_align_interface.h:378:
> instantiated from 'TScoreValue seqan::localAlignment(const  
> TStringSet&, const
> seqan::Score<TScoreValue, TScoreSpec>&, TTag) [with TStringSet =
> seqan::Align<seqan::String<seqan::SimpleType<unsigned char,  
> seqan::AminoAcid_>,
> seqan::Alloc<void> >, seqan::ArrayGaps>, TScoreValue = int, TSpec =
> seqan::ScoreMatrix<seqan::SimpleType<unsigned char,  
> seqan::AminoAcid_>,
> seqan::Blosum62_>, TTag = seqan::Tag<seqan::SmithWaterman_>]'
> alignment_local.cpp:65:   instantiated from here
> /home/yyang/bin/seqan/seqan/score/score_base.h:206: error: no match  
> for
> 'operator[]' in 'seq1[pos1]'
> /home/yyang/bin/seqan/seqan/score/score_base.h:206: error: no match  
> for
> 'operator[]' in 'seq2[pos2]'
>
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--
Manuel Holtgrewe			manuel.holtgrewe@fu-berlin.de
Freie Universität Berlin		http://www.inf.fu-berlin.de/
Institut für Informatik			Phone: +49 30 838 75246
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