[Seqan-dev] local alignment with blosum scoring matrix
- From: Young-ik Yang <maemukki@yahoo.com>
- To: seqan-dev@lists.fu-berlin.de
- Date: Fri, 5 Aug 2011 08:30:49 -0700 (PDT)
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- Reply-to: SeqAn Development <seqan-dev@lists.fu-berlin.de>
- Subject: [Seqan-dev] local alignment with blosum scoring matrix
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]'
