|
RNAlib-2.4.17
|
|
Various utility- and helper-functions for sequence alignments and comparative structure prediction. More...
Include dependency graph for alignments.h:
This graph shows which files directly or indirectly include this file:Go to the source code of this file.
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. | |
| 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... | |
| 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... | |
| 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... | |
Various utility- and helper-functions for sequence alignments and comparative structure prediction.
,