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

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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
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