Utilities to deal with Nucleotide Alphabets

Functions to cope with various aspects related to the nucleotide sequence alphabet.

Defines

VRNA_SEQUENCE_RNA

#include <ViennaRNA/sequence.h>

VRNA_SEQUENCE_DNA

#include <ViennaRNA/sequence.h>

Typedefs

typedef struct vrna_sequence_s vrna_seq_t

#include <ViennaRNA/sequence.h>

Typename for nucleotide sequence representation data structure vrna_sequence_s.

typedef struct vrna_alignment_s vrna_msa_t

#include <ViennaRNA/sequence.h>

Enums

enum vrna_seq_type_e

A enumerator used in vrna_sequence_s to distinguish different nucleotide sequences.

Values:

enumerator VRNA_SEQ_UNKNOWN

Nucleotide sequence represents an Unkown type.

enumerator VRNA_SEQ_RNA

Nucleotide sequence represents an RNA type.

enumerator VRNA_SEQ_DNA

Nucleotide sequence represents a DNA type.

Functions

unsigned int vrna_sequence_length_max(unsigned int options)

#include <ViennaRNA/alphabet.h>

int vrna_nucleotide_IUPAC_identity(char a, char b)

#include <ViennaRNA/alphabet.h>

void vrna_ptypes_prepare(vrna_fold_compound_t *fc, unsigned int options)

#include <ViennaRNA/alphabet.h>

char *vrna_ptypes(const short *S, vrna_md_t *md)

#include <ViennaRNA/alphabet.h>

Get an array of the numerical encoding for each possible base pair (i,j)

See also

vrna_idx_col_wise(), vrna_fold_compound_t

Note

This array is always indexed in column-wise order, in contrast to previously different indexing between mfe and pf variants!

short *vrna_seq_encode(const char *sequence, vrna_md_t *md)

#include <ViennaRNA/alphabet.h>

Get a numerical representation of the nucleotide sequence.

SWIG Wrapper Notes:

In the target scripting language, this function is wrapped as overloaded function seq_encode() where the last parameter, the model_details data structure, is optional. If it is omitted, default model settings are applied, i.e. default nucleotide letter conversion. The wrapped function returns a list/tuple of integer representations of the input sequence. See, e.g. RNA.seq_encode() in the Python API.

Parameters:

• sequence – The input sequence in upper-case letters

• md – A pointer to a vrna_md_t data structure that specifies the conversion type

Returns:

A list of integer encodings for each sequence letter (1-based). Position 0 denotes the length of the list

short *vrna_seq_encode_simple(const char *sequence, vrna_md_t *md)

#include <ViennaRNA/alphabet.h>

Get a numerical representation of the nucleotide sequence (simple version)

int vrna_nucleotide_encode(char c, vrna_md_t *md)

#include <ViennaRNA/alphabet.h>

Encode a nucleotide character to numerical value.

This function encodes a nucleotide character to its numerical representation as required by many functions in RNAlib.

See also

vrna_nucleotide_decode(), vrna_seq_encode()

Parameters:

• c – The nucleotide character to encode

• md – The model details that determine the kind of encoding

Returns:

The encoded nucleotide

char vrna_nucleotide_decode(int enc, vrna_md_t *md)

#include <ViennaRNA/alphabet.h>

Decode a numerical representation of a nucleotide back into nucleotide alphabet.

This function decodes a numerical representation of a nucleotide character back into nucleotide alphabet

See also

vrna_nucleotide_encode(), vrna_seq_encode()

Parameters:

• enc – The encoded nucleotide

• md – The model details that determine the kind of decoding

Returns:

The decoded nucleotide character

void vrna_aln_encode(const char *sequence, short **S_p, short **s5_p, short **s3_p, char **ss_p, unsigned int **as_p, vrna_md_t *md)

#include <ViennaRNA/alphabet.h>

unsigned int vrna_get_ptype_md(int i, int j, vrna_md_t *md)

#include <ViennaRNA/alphabet.h>

unsigned int vrna_get_ptype(int ij, char *ptype)

#include <ViennaRNA/alphabet.h>

unsigned int vrna_get_ptype_window(int i, int j, char **ptype)

#include <ViennaRNA/alphabet.h>

vrna_seq_t *vrna_sequence(const char *string, unsigned int options)

#include <ViennaRNA/sequence.h>

int vrna_sequence_add(vrna_fold_compound_t *fc, const char *string, unsigned int options)

#include <ViennaRNA/sequence.h>

int vrna_sequence_remove(vrna_fold_compound_t *fc, unsigned int i)

#include <ViennaRNA/sequence.h>

void vrna_sequence_remove_all(vrna_fold_compound_t *fc)

#include <ViennaRNA/sequence.h>

void vrna_sequence_prepare(vrna_fold_compound_t *fc)

#include <ViennaRNA/sequence.h>

int vrna_sequence_order_update(vrna_fold_compound_t *fc, const unsigned int *order)

#include <ViennaRNA/sequence.h>

int vrna_msa_add(vrna_fold_compound_t *fc, const char **alignment, const char **names, const unsigned char *orientation, const unsigned long long *start, const unsigned long long *genome_size, unsigned int options)

#include <ViennaRNA/sequence.h>

struct vrna_sequence_s

#include <ViennaRNA/sequence.h>

Data structure representing a nucleotide sequence.

Public Members

vrna_seq_type_e type

The type of sequence.

char *name

char *string

The string representation of the sequence.

short *encoding

The integer representation of the sequence.

short *encoding5

short *encoding3

unsigned int length

The length of the sequence.

struct vrna_alignment_s

Public Members

unsigned int n_seq

vrna_seq_t *sequences

char **gapfree_seq

unsigned int *gapfree_size

unsigned long long *genome_size

unsigned long long *start

unsigned char *orientation

unsigned int **a2s