Utilities to deal with Nucleotide Alphabets

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

Detailed Description

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

Collaboration diagram for Utilities to deal with Nucleotide Alphabets:

Files
file	alphabet.h
	Functions to process, convert, and generally handle different nucleotide and/or base pair alphabets.
file	sequence.h
	Functions and data structures related to sequence representations ,.

Data Structures
struct	vrna_sequence_s
	Data structure representing a nucleotide sequence. More...
struct	vrna_alignment_s

Typedefs
typedef struct vrna_sequence_s	vrna_seq_t
	Typename for nucleotide sequence representation data structure vrna_sequence_s.

Enumerations

Functions
char *	vrna_ptypes (const short *S, vrna_md_t *md)
	Get an array of the numerical encoding for each possible base pair (i,j) More...
short *	vrna_seq_encode (const char *sequence, vrna_md_t *md)
	Get a numerical representation of the nucleotide sequence.
short *	vrna_seq_encode_simple (const char *sequence, vrna_md_t *md)
	Get a numerical representation of the nucleotide sequence (simple version)
int	vrna_nucleotide_encode (char c, vrna_md_t *md)
	Encode a nucleotide character to numerical value. More...
char	vrna_nucleotide_decode (int enc, vrna_md_t *md)
	Decode a numerical representation of a nucleotide back into nucleotide alphabet. More...

---

Data Structure Documentation

struct vrna_sequence_s

Data structure representing a nucleotide sequence.

Data Fields
vrna_seq_type_e	type
	The type of sequence.
char *	string
	The string representation of the sequence.
short *	encoding
	The integer representation of the sequence.
unsigned int	length
	The length of the sequence.

struct vrna_alignment_s

Collaboration diagram for vrna_alignment_s:

Enumeration Type Documentation

enum vrna_seq_type_e

#include <ViennaRNA/sequence.h>

A enumerator used in vrna_sequence_s to distinguish different nucleotide sequences.

Enumerator
VRNA_SEQ_UNKNOWN	Nucleotide sequence represents an Unkown type.
VRNA_SEQ_RNA	Nucleotide sequence represents an RNA type.
VRNA_SEQ_DNA	Nucleotide sequence represents a DNA type.

Function Documentation

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)

Note

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

See also

vrna_idx_col_wise(), vrna_fold_compound_t

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