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RNAlib-2.4.17
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Functions to extract features from and to manipulate multiple sequence alignments. More...
Functions to extract features from and to manipulate multiple sequence alignments.
Collaboration diagram for Multiple Sequence Alignment Utilities:Modules | |
| Deprecated Interface for Multiple Sequence Alignment Utilities | |
Files | |
| file | alignments.h |
| Various utility- and helper-functions for sequence alignments and comparative structure prediction. | |
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. | |
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... | |
| 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/utils/alignments.h>
Flag indicating Shannon Entropy measure.
Shannon Entropy is defined as
| int vrna_aln_mpi | ( | const char ** | alignment | ) |
#include <ViennaRNA/utils/alignments.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/utils/alignments.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/utils/alignments.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/utils/alignments.h>
Free memory occupied by a set of aligned sequences.
| alignment | The input alignment |
| char** vrna_aln_uppercase | ( | const char ** | alignment | ) |
#include <ViennaRNA/utils/alignments.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/utils/alignments.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/utils/alignments.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/utils/alignments.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.pair 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/utils/alignments.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. | char* vrna_aln_consensus_sequence | ( | const char ** | alignment, |
| const vrna_md_t * | md_p | ||
| ) |
#include <ViennaRNA/utils/alignments.h>
Compute the consensus sequence for a given multiple sequence alignment.
| alignment | The input sequence alignment (last entry must be NULL terminated) |
| md_p | Model details that specify known nucleotides (Maybe NULL) |
| char* vrna_aln_consensus_mis | ( | const char ** | alignment, |
| const vrna_md_t * | md_p | ||
| ) |
#include <ViennaRNA/utils/alignments.h>
Compute the Most Informative Sequence (MIS) for a given multiple sequence alignment.
The most informative sequence (MIS) [9] displays for each alignment column the nucleotides with frequency greater than the background frequency, projected into IUPAC notation. Columns where gaps are over-represented are in lower case.
| alignment | The input sequence alignment (last entry must be NULL terminated) |
| md_p | Model details that specify known nucleotides (Maybe NULL) |