Functions to extract features from and to manipulate multiple sequence alignments. More...

Detailed Description

Functions to extract features from and to manipulate multiple sequence alignments.

Collaboration diagram for Multiple Sequence Alignment Utilities:

Modules
	Deprecated Interface for Multiple Sequence Alignment Utilities

Files
file	alignments.h
	Various utility- and helper-functions for sequence alignments and comparative structure prediction.

Data Structures
struct	vrna_pinfo_s
	A base pair info structure. More...

Macros
#define	VRNA_ALN_DEFAULT 0U
	Use default alignment settings.

#define	VRNA_ALN_RNA 1U
	Convert to RNA alphabet.

#define	VRNA_ALN_DNA 2U
	Convert to DNA alphabet.

#define	VRNA_ALN_UPPERCASE 4U
	Convert to uppercase nucleotide letters.

#define	VRNA_ALN_LOWERCASE 8U
	Convert to lowercase nucleotide letters.

#define	VRNA_MEASURE_SHANNON_ENTROPY 1U
	Flag indicating Shannon Entropy measure. More...

Typedefs
typedef struct vrna_pinfo_s	vrna_pinfo_t
	Typename for the base pair info repesenting data structure vrna_pinfo_s.

Functions
int	vrna_aln_mpi (const char **alignment)
	Get the mean pairwise identity in steps from ?to?(ident) More...

vrna_pinfo_t *	vrna_aln_pinfo (vrna_fold_compound_t vc, const char structure, double threshold)
	Retrieve an array of vrna_pinfo_t structures from precomputed pair probabilities. More...

char **	vrna_aln_slice (const char **alignment, unsigned int i, unsigned int j)
	Slice out a subalignment from a larger alignment. More...

void	vrna_aln_free (char **alignment)
	Free memory occupied by a set of aligned sequences. More...

char **	vrna_aln_uppercase (const char **alignment)
	Create a copy of an alignment with only uppercase letters in the sequences. More...

char **	vrna_aln_toRNA (const char **alignment)
	Create a copy of an alignment where DNA alphabet is replaced by RNA alphabet. More...

char **	vrna_aln_copy (const char **alignment, unsigned int options)
	Make a copy of a multiple sequence alignment. More...

float *	vrna_aln_conservation_struct (const char *alignment, const char structure, const vrna_md_t *md)
	Compute base pair conservation of a consensus structure. More...

float *	vrna_aln_conservation_col (const char *alignment, const vrna_md_t md_p, unsigned int options)
	Compute nucleotide conservation in an alignment. More...

char *	vrna_aln_consensus_sequence (const char *alignment, const vrna_md_t md_p)
	Compute the consensus sequence for a given multiple sequence alignment. More...

char *	vrna_aln_consensus_mis (const char *alignment, const vrna_md_t md_p)
	Compute the Most Informative Sequence (MIS) for a given multiple sequence alignment. More...

Data Structure Documentation

struct vrna_pinfo_s

A base pair info structure.

For each base pair (i,j) with i,j in [0, n-1] the structure lists:

its probability 'p'
an entropy-like measure for its well-definedness 'ent'
the frequency of each type of pair in 'bp[]'
- 'bp[0]' contains the number of non-compatible sequences
- 'bp[1]' the number of CG pairs, etc.

Data Fields
unsigned	i
	nucleotide position i

unsigned	j
	nucleotide position j

float	p
	Probability.

float	ent
	Pseudo entropy for .

short	bp [8]
	Frequencies of pair_types.

char	comp
	1 iff pair is in mfe structure

Macro Definition Documentation

#define VRNA_MEASURE_SHANNON_ENTROPY 1U

#include <ViennaRNA/utils/alignments.h>

Flag indicating Shannon Entropy measure.

Shannon Entropy is defined as $H = - \sum_c p_c \cdot \log_2 p_c$

Function Documentation

int vrna_aln_mpi ( const char ** alignment )

#include <ViennaRNA/utils/alignments.h>

Get the mean pairwise identity in steps from ?to?(ident)

Parameters

alignment Aligned sequences

Returns: The mean pairwise identity

vrna_pinfo_t* vrna_aln_pinfo	(	vrna_fold_compound_t *	vc,
		const char *	structure,
		double	threshold
	)

#include <ViennaRNA/utils/alignments.h>

Retrieve an array of vrna_pinfo_t structures from precomputed pair probabilities.

This array of structures contains information about positionwise pair probabilies, base pair entropy and more

See also: vrna_pinfo_t, and vrna_pf()

Parameters

vc	The vrna_fold_compound_t of type VRNA_FC_TYPE_COMPARATIVE with precomputed partition function matrices
structure	An optional structure in dot-bracket notation (Maybe NULL)
threshold	Do not include results with pair probabilities below threshold

Returns: The vrna_pinfo_t array

char** vrna_aln_slice	(	const char **	alignment,
		unsigned int	i,
		unsigned int	j
	)

#include <ViennaRNA/utils/alignments.h>

Slice out a subalignment from a larger alignment.

Note: The user is responsible to free the memory occupied by the returned subalignment

See also: vrna_aln_free()

Parameters

alignment	The input alignment
i	The first column of the subalignment (1-based)
j	The last column of the subalignment (1-based)

Returns: The subalignment between column and

void vrna_aln_free ( char ** alignment )

#include <ViennaRNA/utils/alignments.h>

Free memory occupied by a set of aligned sequences.

Parameters

alignment The input alignment

char** vrna_aln_uppercase ( const char ** alignment )

#include <ViennaRNA/utils/alignments.h>

Create a copy of an alignment with only uppercase letters in the sequences.

See also: vrna_aln_copy

Parameters

alignment The input sequence alignment (last entry must be NULL terminated)

Returns: A copy of the input alignment where lowercase sequence letters are replaced by uppercase letters

char** vrna_aln_toRNA ( const char ** alignment )

#include <ViennaRNA/utils/alignments.h>

Create a copy of an alignment where DNA alphabet is replaced by RNA alphabet.

See also: vrna_aln_copy

Parameters

alignment The input sequence alignment (last entry must be NULL terminated)

Returns: A copy of the input alignment where DNA alphabet is replaced by RNA alphabet (T -> U)

char** vrna_aln_copy	(	const char **	alignment,
		unsigned int	options
	)

#include <ViennaRNA/utils/alignments.h>

Make a copy of a multiple sequence alignment.

This function allows one to create a copy of a multiple sequence alignment. The options parameter additionally allows for sequence manipulation, such as converting DNA to RNA alphabet, and conversion to uppercase letters.

See also: vrna_aln_copy(), VRNA_ALN_RNA, VRNA_ALN_UPPERCASE, VRNA_ALN_DEFAULT

Parameters

alignment	The input sequence alignment (last entry must be NULL terminated)
options	Option flags indicating whether the aligned sequences should be converted

Returns: A (manipulated) copy of the input alignment

float * vrna_aln_conservation_struct	(	const char **	alignment,
		const char *	structure,
		const vrna_md_t *	md
	)

#include <ViennaRNA/utils/alignments.h>

Compute base pair conservation of a consensus structure.

This function computes the base pair conservation (fraction of canonical base pairs) of a consensus structure given a multiple sequence alignment. The base pair types that are considered canonical may be specified using the vrna_md_t.pair array. Passing NULL as parameter md results in default pairing rules, i.e. canonical Watson-Crick and GU Wobble pairs.

Parameters

alignment	The input sequence alignment (last entry must be NULL terminated)
structure	The consensus structure in dot-bracket notation
md	Model details that specify compatible base pairs (Maybe NULL)

Returns: A 1-based vector of base pair conservations

SWIG Wrapper Notes:: This function is available in an overloaded form where the last parameter may be omitted, indicating md = NULL

float * vrna_aln_conservation_col	(	const char **	alignment,
		const vrna_md_t *	md,
		unsigned int	options
	)

#include <ViennaRNA/utils/alignments.h>

Compute nucleotide conservation in an alignment.

This function computes the conservation of nucleotides in alignment columns. The simples measure is Shannon Entropy and can be selected by passing the VRNA_MEASURE_SHANNON_ENTROPY flag in the options parameter.

Note: Currently, only VRNA_MEASURE_SHANNON_ENTROPY is supported as conservation measure.

See also: VRNA_MEASURE_SHANNON_ENTROPY

Parameters

alignment	The input sequence alignment (last entry must be NULL terminated)
md	Model details that specify known nucleotides (Maybe NULL)
options	A flag indicating which measure of conservation should be applied

Returns: A 1-based vector of column conservations

SWIG Wrapper Notes:: This function is available in an overloaded form where the last two parameters may be omitted, indicating md = NULL, and options = VRNA_MEASURE_SHANNON_ENTROPY, respectively.

char* vrna_aln_consensus_sequence	(	const char **	alignment,
		const vrna_md_t *	md_p
	)

#include <ViennaRNA/utils/alignments.h>

Compute the consensus sequence for a given multiple sequence alignment.

Parameters

alignment	The input sequence alignment (last entry must be NULL terminated)
md_p	Model details that specify known nucleotides (Maybe NULL)

Returns: The consensus sequence of the alignment, i.e. the most frequent nucleotide for each alignment column

char* vrna_aln_consensus_mis	(	const char **	alignment,
		const vrna_md_t *	md_p
	)

#include <ViennaRNA/utils/alignments.h>

Compute the Most Informative Sequence (MIS) for a given multiple sequence alignment.

The most informative sequence (MIS) [9] displays for each alignment column the nucleotides with frequency greater than the background frequency, projected into IUPAC notation. Columns where gaps are over-represented are in lower case.

Parameters

alignment	The input sequence alignment (last entry must be NULL terminated)
md_p	Model details that specify known nucleotides (Maybe NULL)

Returns: The most informative sequence for the alignment

Detailed Description

Modules

Files

Data Structures

Macros

Typedefs

Functions

Data Structure Documentation

Data Fields

Macro Definition Documentation

Function Documentation