Deprecated Interface for Multiple Sequence Alignment Utilities

Typedefs

typedef struct vrna_pinfo_s pair_info

Old typename of vrna_pinfo_s. 

#include <ViennaRNA/sequences/alignments.h>

Deprecated:

Use vrna_pinfo_t instead!

Functions

int read_clustal(FILE *clust, char *AlignedSeqs[], char *names[])
#include <ViennaRNA/sequences/alignments.h>
char *consensus(const char *AS[])
#include <ViennaRNA/sequences/alignments.h>
char *consens_mis(const char *AS[])
#include <ViennaRNA/sequences/alignments.h>
char *get_ungapped_sequence(const char *seq)
#include <ViennaRNA/sequences/alignments.h>
int get_mpi(char *Alseq[], int n_seq, int length, int *mini)

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

#include <ViennaRNA/sequences/alignments.h>

Deprecated:

Use vrna_aln_mpi() as a replacement

Parameters:

  • Alseq

  • n_seq – The number of sequences in the alignment

  • length – The length of the alignment

  • mini

Returns:

The mean pairwise identity

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. 

#include <ViennaRNA/sequences/alignments.h>

this function assumes that in S, S5, s3, ss and as enough space is already allocated (size must be at least sequence length+2)

Parameters:

  • sequence – The gapped sequence from the alignment

  • S – pointer to an array that holds encoded sequence

  • s5 – pointer to an array that holds the next base 5’ of alignment position i

  • s3 – pointer to an array that holds the next base 3’ of alignment position i

  • ss

  • as

  • circ – assume the molecules to be circular instead of linear (circ=0)

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. 

#include <ViennaRNA/sequences/alignments.h>

Note that these arrays will also be initialized according to the sequence alignment given

See also

free_sequence_arrays()

Parameters:

  • sequences – The aligned sequences

  • S – A pointer to the array of encoded sequences

  • S5 – A pointer to the array that contains the next 5’ nucleotide of a sequence position

  • S3 – A pointer to the array that contains the next 3’ nucleotide of a sequence position

  • a2s – A pointer to the array that contains the alignment to sequence position mapping

  • Ss – A pointer to the array that contains the ungapped sequence

  • circ – assume the molecules to be circular instead of linear (circ=0)

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. 

#include <ViennaRNA/sequences/alignments.h>

This function frees the memory previously allocated with alloc_sequence_arrays()

See also

alloc_sequence_arrays()

Parameters:

  • n_seq – The number of aligned sequences

  • S – A pointer to the array of encoded sequences

  • S5 – A pointer to the array that contains the next 5’ nucleotide of a sequence position

  • S3 – A pointer to the array that contains the next 3’ nucleotide of a sequence position

  • a2s – A pointer to the array that contains the alignment to sequence position mapping

  • Ss – A pointer to the array that contains the ungapped sequence