ost::seq::alg Namespace Reference

Namespaces
namespace	mat
Data Structures
struct	AlignmentOpts
	options for local and global sequence alignment algorithms More...
class	InsDel
	get insertions and deletions of an alignment More...
struct	AlignedPatch
	holds the result of a local sequence alignment More...
struct	RefMode
class	SubstWeightMatrix
	position-independet substitution weight matrix More...
Typedefs
typedef std::vector< AlignedPatch >	AlignedPatchList
typedef boost::shared_ptr < SubstWeightMatrix >	SubstWeightMatrixPtr
Functions
std::vector< Real > DLLEXPORT_OST_SEQ_ALG	Conservation (const AlignmentHandle &aln, bool assign=true, const String &prop_name="cons")
AlignmentHandle DLLEXPORT_OST_SEQ_ALG	GlobalSequenceAlign (const SequenceHandle &seq_a, const SequenceHandle &seq_b, const AlignmentOpts &opts)
AlignedPatchList DLLEXPORT_OST_SEQ_ALG	LocalSequenceAlign (const SequenceHandle &seq_a, const SequenceHandle &seq_b, const AlignmentOpts &opts)
AlignmentHandle DLLEXPORT_OST_SEQ_ALG	MergePairwiseAlignments (const AlignmentList &pairwise_alns, const SequenceHandle &ref_seq)
Real DLLEXPORT_OST_SEQ_ALG	SequenceIdentity (const AlignmentHandle &aln, RefMode::Type ref_mode=RefMode::LONGER_SEQUENCE, int seq_a=0, int seq_b=1)
SubstWeightMatrixPtr DLLEXPORT_OST_SEQ_ALG	SubstWeightMatrixFromInfo (const info::InfoGroup &group)
void DLLEXPORT_OST_SEQ_ALG	SubstWeightMatrixToInfo (const SubstWeightMatrixPtr &subst_mat, info::InfoGroup &group)

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Typedef Documentation

typedef std::vector<AlignedPatch> AlignedPatchList

Definition at line 50 of file local_align.hh.

typedef boost::shared_ptr<SubstWeightMatrix> SubstWeightMatrixPtr

Definition at line 32 of file subst_weight_matrix.hh.

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Function Documentation

std::vector<Real> DLLEXPORT_OST_SEQ_ALG ost::seq::alg::Conservation	(	const AlignmentHandle &	aln,
		bool	assign = true,
		const String &	prop_name = "cons"
	)

Calculates conservation scores for each column in the alignment.

The conservation score is a value between 0 and 1. The bigger the number the more conserved the aligned residues are.

assign If true, the conservation scores are assigned to attached residues. The name of the property can be changed with the prop_name parameter. Useful when coloring entities based on sequence conservation. prop_name The property name for assigning the conservation to attached residues. Defaults to 'cons'.

AlignmentHandle DLLEXPORT_OST_SEQ_ALG ost::seq::alg::GlobalSequenceAlign	(	const SequenceHandle &	seq_a,
		const SequenceHandle &	seq_b,
		const AlignmentOpts &	opts
	)

globally align two sequences

the optimal global alignment of the two sequences, given the substitution weights and gap opening penalties is computed by using a classical Needleman-Wunsch algorithm. The algorithm has O(n*m) complexity in both space and time.

AlignedPatchList DLLEXPORT_OST_SEQ_ALG ost::seq::alg::LocalSequenceAlign	(	const SequenceHandle &	seq_a,
		const SequenceHandle &	seq_b,
		const AlignmentOpts &	opts
	)

Align pair of sequences locally with Waterman-Smith algorithm.

The alignment algorithm will return the set of optimal alignments given the weights of the substitution matrix and gap opening and extension penalties. The sequence patches are non-overlapping

Parameters:

	seq_a	is the first sequence to be aligned
	seq_b	is the second sequence to be aligned
	opts	holds a set of alignment options such as gap opening and extension penalties and the substitution matrix

Returns:

list of locally aligned sequence patches.

AlignmentHandle DLLEXPORT_OST_SEQ_ALG ost::seq::alg::MergePairwiseAlignments	(	const AlignmentList &	pairwise_alns,
		const SequenceHandle &	ref_seq
	)

merge a list of pairwise alignments into one multiple sequence alignment

All sequences in the pairwise sequence alignments are a realigned to the reference sequence. This is useful to merge the results of a BLAST or HMM database search into one multiple sequence alignment.

The method does not produce the optimal multiple sequence alignemnt for all the sequences.

Parameters:

	pairwise_alignments	is a list of AlignmentHandles, each containing two sequences
	ref_seq	is the reference sequence. The reference sequence must not contain any gaps.

Real DLLEXPORT_OST_SEQ_ALG ost::seq::alg::SequenceIdentity	(	const AlignmentHandle &	aln,
		RefMode::Type	ref_mode = RefMode::LONGER_SEQUENCE,
		int	seq_a = 0,
		int	seq_b = 1
	)

calculate sequence identity for two sequences in an alignment

Parameters:

	ref_mode	influences the way the sequence identity is calculated. When set to LONGER_SEQUENCE, the sequence identity is calculated as the number of matches divided by the length of the longer sequence. If set to ALIGNMENT, the sequence identity is calculated as the number of matches divided by the number of aligned residues.
	seq_a	is the index of the first sequence
	seq_b	is the index of the second sequence
	aln	is the sequence alignment

Returns:

sequence identity in the range 0 to 100

SubstWeightMatrixPtr DLLEXPORT_OST_SEQ_ALG ost::seq::alg::SubstWeightMatrixFromInfo

(

const info::InfoGroup &

group

)

void DLLEXPORT_OST_SEQ_ALG ost::seq::alg::SubstWeightMatrixToInfo	(	const SubstWeightMatrixPtr &	subst_mat,
		info::InfoGroup &	group
	)