alignments.h File Reference

Various utility- and helper-functions for sequence alignments and comparative structure prediction. More...

Include dependency graph for alignments.h:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

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.
typedef struct vrna_pinfo_s	pair_info
	Old typename of vrna_pinfo_s. More...

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...
int	get_mpi (char *Alseq[], int n_seq, int length, int *mini)
	Get the mean pairwise identity in steps from ?to?(ident) More...
void	encode_ali_sequence (const char *sequence, short *S, short *s5, short *s3, char *ss, unsigned short *as, int circ)
	Get arrays with encoded sequence of the alignment. More...
void	alloc_sequence_arrays (const char **sequences, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss, int circ)
	Allocate memory for sequence array used to deal with aligned sequences. More...
void	free_sequence_arrays (unsigned int n_seq, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss)
	Free the memory of the sequence arrays used to deal with aligned sequences. More...

Detailed Description

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

,