RNAlib-2.4.4
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Data Structures | |
struct | vrna_pinfo_s |
A base pair info structure. More... | |
Macros | |
#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... | |
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... | |
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:
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 | |
#define VRNA_MEASURE_SHANNON_ENTROPY 1U |
#include <ViennaRNA/aln_util.h>
Flag indicating Shannon Entropy measure.
Shannon Entropy is defined as
typedef struct vrna_pinfo_s pair_info |
int vrna_aln_mpi | ( | const char ** | alignment | ) |
#include <ViennaRNA/aln_util.h>
Get the mean pairwise identity in steps from ?to?(ident)
alignment | Aligned sequences |
vrna_pinfo_t* vrna_aln_pinfo | ( | vrna_fold_compound_t * | vc, |
const char * | structure, | ||
double | threshold | ||
) |
#include <ViennaRNA/aln_util.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
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 |
char** vrna_aln_slice | ( | const char ** | alignment, |
unsigned int | i, | ||
unsigned int | j | ||
) |
#include <ViennaRNA/aln_util.h>
Slice out a subalignment from a larger alignment.
alignment | The input alignment |
i | The first column of the subalignment (1-based) |
j | The last column of the subalignment (1-based) |
void vrna_aln_free | ( | char ** | alignment | ) |
#include <ViennaRNA/aln_util.h>
Free memory occupied by a set of aligned sequences.
alignment | The input alignment |
char** vrna_aln_uppercase | ( | const char ** | alignment | ) |
#include <ViennaRNA/aln_util.h>
Create a copy of an alignment with only uppercase letters in the sequences.
alignment | The input sequence alignment (last entry must be NULL terminated) |
char** vrna_aln_toRNA | ( | const char ** | alignment | ) |
#include <ViennaRNA/aln_util.h>
Create a copy of an alignment where DNA alphabet is replaced by RNA alphabet.
alignment | The input sequence alignment (last entry must be NULL terminated) |
char** vrna_aln_copy | ( | const char ** | alignment, |
unsigned int | options | ||
) |
#include <ViennaRNA/aln_util.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.
alignment | The input sequence alignment (last entry must be NULL terminated) |
options | Option flags indicating whether the aligned sequences should be converted |
float * vrna_aln_conservation_struct | ( | const char ** | alignment, |
const char * | structure, | ||
const vrna_md_t * | md | ||
) |
#include <ViennaRNA/aln_util.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.pairs array. Passing NULL as parameter md
results in default pairing rules, i.e. canonical Watson-Crick and GU Wobble pairs.
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) |
md
= NULL float * vrna_aln_conservation_col | ( | const char ** | alignment, |
const vrna_md_t * | md, | ||
unsigned int | options | ||
) |
#include <ViennaRNA/aln_util.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.
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 |
md
= NULL, and options
= VRNA_MEASURE_SHANNON_ENTROPY, respectively. int get_mpi | ( | char * | Alseq[], |
int | n_seq, | ||
int | length, | ||
int * | mini | ||
) |
#include <ViennaRNA/aln_util.h>
Get the mean pairwise identity in steps from ?to?(ident)
Alseq | |
n_seq | The number of sequences in the alignment |
length | The length of the alignment |
mini |
void encode_ali_sequence | ( | const char * | sequence, |
short * | S, | ||
short * | s5, | ||
short * | s3, | ||
char * | ss, | ||
unsigned short * | as, | ||
int | circ | ||
) |
#include <ViennaRNA/aln_util.h>
Get arrays with encoded sequence of the alignment.
this function assumes that in S, S5, s3, ss and as enough space is already allocated (size must be at least sequence length+2)
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 | ||
) |
#include <ViennaRNA/aln_util.h>
Allocate memory for sequence array used to deal with aligned sequences.
Note that these arrays will also be initialized according to the sequence alignment given
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 | ||
) |
#include <ViennaRNA/aln_util.h>
Free the memory of the sequence arrays used to deal with aligned sequences.
This function frees the memory previously allocated with alloc_sequence_arrays()
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 |