Support of modified bases in secondary structure prediction. More...
Support of modified bases in secondary structure prediction.
Energy parameter corrections for modified bases.
Many RNAs are known to be (heavily) modified post-trasnciptionaly. The best known examples are tRNAs and rRNAs. To-date, more than 150 different modifications are listed in the MODOMICS database (http://genesilico.pl/modomics/) [5].
Many of the modified bases change the pairing behavior compared to their unmodified version, affecting not only the pairing partner preference, but also the resulting stability of the loops the base pairs may form.
Here, we provide a simple soft constraints callback implementation to correct for some well known modified bases where energy parameters are available for. This mechanism also supports arbitrary new modified base energy parameters supplied in JSON format (see JSON Parameter Files for Modified Bases for details).
Files | |
file | soft_special.h |
Specialized implementations that utilize the soft constraint callback mechanism. | |
Macros | |
#define | VRNA_SC_MOD_CHECK_FALLBACK 1 |
Check for sequence positions whether they resemble the fallback base. | |
#define | VRNA_SC_MOD_CHECK_UNMOD 2 |
Check for sequence positions whether they resemble the unmodified base. | |
#define | VRNA_SC_MOD_SILENT 4 |
Do not produce any warnings within the vrna_sc_mod*() functions. | |
#define | VRNA_SC_MOD_DEFAULT (VRNA_SC_MOD_CHECK_FALLBACK | VRNA_SC_MOD_CHECK_UNMOD) |
Default settings for the vrna_sc_mod*() functions. | |
Typedefs | |
typedef struct vrna_sc_mod_param_s * | vrna_sc_mod_param_t |
Modified base parameter data structure. | |
Functions | |
vrna_sc_mod_param_t | vrna_sc_mod_read_from_jsonfile (const char *filename, vrna_md_t *md) |
Parse and extract energy parameters for a modified base from a JSON file. | |
vrna_sc_mod_param_t | vrna_sc_mod_read_from_json (const char *json, vrna_md_t *md) |
Parse and extract energy parameters for a modified base from a JSON string. | |
void | vrna_sc_mod_parameters_free (vrna_sc_mod_param_t params) |
Release memory occupied by a modified base parameter data structure. | |
int | vrna_sc_mod_json (vrna_fold_compound_t *fc, const char *json, const unsigned int *modification_sites, unsigned int options) |
Prepare soft constraint callbacks for modified base as specified in JSON string. | |
int | vrna_sc_mod_jsonfile (vrna_fold_compound_t *fc, const char *json_file, const unsigned int *modification_sites, unsigned int options) |
Prepare soft constraint callbacks for modified base as specified in JSON string. | |
int | vrna_sc_mod (vrna_fold_compound_t *fc, const vrna_sc_mod_param_t params, const unsigned int *modification_sites, unsigned int options) |
Prepare soft constraint callbacks for modified base as specified in JSON string. | |
int | vrna_sc_mod_m6A (vrna_fold_compound_t *fc, const unsigned int *modification_sites, unsigned int options) |
Add soft constraint callbacks for N6-methyl-adenosine (m6A) | |
int | vrna_sc_mod_pseudouridine (vrna_fold_compound_t *fc, const unsigned int *modification_sites, unsigned int options) |
Add soft constraint callbacks for Pseudouridine. | |
int | vrna_sc_mod_inosine (vrna_fold_compound_t *fc, const unsigned int *modification_sites, unsigned int options) |
Add soft constraint callbacks for Inosine. | |
int | vrna_sc_mod_7DA (vrna_fold_compound_t *fc, const unsigned int *modification_sites, unsigned int options) |
Add soft constraint callbacks for 7-deaza-adenosine (7DA) | |
int | vrna_sc_mod_purine (vrna_fold_compound_t *fc, const unsigned int *modification_sites, unsigned int options) |
Add soft constraint callbacks for Purine (a.k.a. nebularine) | |
int | vrna_sc_mod_dihydrouridine (vrna_fold_compound_t *fc, const unsigned int *modification_sites, unsigned int options) |
Add soft constraint callbacks for dihydrouridine. | |
#define VRNA_SC_MOD_CHECK_FALLBACK 1 |
#include <ViennaRNA/constraints/soft_special.h>
Check for sequence positions whether they resemble the fallback base.
This flag can be used to enable a sanity check within the vrna_sc_mod*() functions to see whether a supposedly modified position actually resembles the fallback base as specified in the modification parameters
#define VRNA_SC_MOD_CHECK_UNMOD 2 |
#include <ViennaRNA/constraints/soft_special.h>
Check for sequence positions whether they resemble the unmodified base.
This flag can be used to enable a sanity check within the vrna_sc_mod*() functions to see whether a supposedly modified position actually resembles the unmodified base as specified in the modification parameters
#define VRNA_SC_MOD_SILENT 4 |
#include <ViennaRNA/constraints/soft_special.h>
Do not produce any warnings within the vrna_sc_mod*() functions.
#define VRNA_SC_MOD_DEFAULT (VRNA_SC_MOD_CHECK_FALLBACK | VRNA_SC_MOD_CHECK_UNMOD) |
#include <ViennaRNA/constraints/soft_special.h>
Default settings for the vrna_sc_mod*() functions.
typedef struct vrna_sc_mod_param_s* vrna_sc_mod_param_t |
#include <ViennaRNA/constraints/soft_special.h>
Modified base parameter data structure.
vrna_sc_mod_param_t vrna_sc_mod_read_from_jsonfile | ( | const char * | filename, |
vrna_md_t * | md | ||
) |
#include <ViennaRNA/constraints/soft_special.h>
Parse and extract energy parameters for a modified base from a JSON file.
filename | The JSON file containing the specifications of the modified base |
md | A model-details data structure (for look-up of canonical base pairs) |
md
parameter may be omitted vrna_sc_mod_param_t vrna_sc_mod_read_from_json | ( | const char * | json, |
vrna_md_t * | md | ||
) |
#include <ViennaRNA/constraints/soft_special.h>
Parse and extract energy parameters for a modified base from a JSON string.
filename | The JSON file containing the specifications of the modified base |
md | A model-details data structure (for look-up of canonical base pairs) |
md
parameter may be omitted void vrna_sc_mod_parameters_free | ( | vrna_sc_mod_param_t | params | ) |
#include <ViennaRNA/constraints/soft_special.h>
Release memory occupied by a modified base parameter data structure.
Properly free a vrna_sc_mod_param_t data structure
params | The data structure to free |
int vrna_sc_mod_json | ( | vrna_fold_compound_t * | fc, |
const char * | json, | ||
const unsigned int * | modification_sites, | ||
unsigned int | options | ||
) |
#include <ViennaRNA/constraints/soft_special.h>
Prepare soft constraint callbacks for modified base as specified in JSON string.
This function prepares all requirements to acknowledge modified bases as specified in the provided json
string. All subsequent predictions will treat each modification site special and adjust energy contributions if necessary.
fc | The fold_compound the corrections should be bound to |
json | The JSON formatted string with the modified base parameters |
modification_sites | A list of modification site, i.e. positions that contain the modified base (1-based, last element in the list indicated by 0) |
options | A bitvector of options how to handle the input, e.g. VRNA_SC_MOD_DEFAULT |
options
= VRNA_SC_MOD_DEFAULT int vrna_sc_mod_jsonfile | ( | vrna_fold_compound_t * | fc, |
const char * | json_file, | ||
const unsigned int * | modification_sites, | ||
unsigned int | options | ||
) |
#include <ViennaRNA/constraints/soft_special.h>
Prepare soft constraint callbacks for modified base as specified in JSON string.
Similar to vrna_sc_mod_json(), this function prepares all requirements to acknowledge modified bases as specified in the provided json
file. All subsequent predictions will treat each modification site special and adjust energy contributions if necessary.
fc | The fold_compound the corrections should be bound to |
json | The JSON formatted string with the modified base parameters |
modification_sites | A list of modification site, i.e. positions that contain the modified base (1-based, last element in the list indicated by 0) |
options
= VRNA_SC_MOD_DEFAULT int vrna_sc_mod | ( | vrna_fold_compound_t * | fc, |
const vrna_sc_mod_param_t | params, | ||
const unsigned int * | modification_sites, | ||
unsigned int | options | ||
) |
#include <ViennaRNA/constraints/soft_special.h>
Prepare soft constraint callbacks for modified base as specified in JSON string.
This function takes a vrna_sc_mod_param_t data structure as obtained from vrna_sc_mod_read_from_json() or vrna_sc_mod_read_from_jsonfile() and prepares all requirements to acknowledge modified bases as specified in the provided params
data structure. All subsequent predictions will treat each modification site special and adjust energy contributions if necessary.
fc | The fold_compound the corrections should be bound to |
json | The JSON formatted string with the modified base parameters |
modification_sites | A list of modification site, i.e. positions that contain the modified base (1-based, last element in the list indicated by 0) |
options | A bitvector of options how to handle the input, e.g. VRNA_SC_MOD_DEFAULT |
options
= VRNA_SC_MOD_DEFAULT int vrna_sc_mod_m6A | ( | vrna_fold_compound_t * | fc, |
const unsigned int * | modification_sites, | ||
unsigned int | options | ||
) |
#include <ViennaRNA/constraints/soft_special.h>
Add soft constraint callbacks for N6-methyl-adenosine (m6A)
This is a convenience wrapper to add support for m6A using the soft constraint callback mechanism. Modification sites are provided as a list of sequence positions (1-based). Energy parameter corrections are derived from [17].
fc | The fold_compound the corrections should be bound to |
modification_sites | A list of modification site, i.e. positions that contain the modified base (1-based, last element in the list indicated by 0) |
options | A bitvector of options how to handle the input, e.g. VRNA_SC_MOD_DEFAULT |
options
= VRNA_SC_MOD_DEFAULT int vrna_sc_mod_pseudouridine | ( | vrna_fold_compound_t * | fc, |
const unsigned int * | modification_sites, | ||
unsigned int | options | ||
) |
#include <ViennaRNA/constraints/soft_special.h>
Add soft constraint callbacks for Pseudouridine.
This is a convenience wrapper to add support for pseudouridine using the soft constraint callback mechanism. Modification sites are provided as a list of sequence positions (1-based). Energy parameter corrections are derived from [15].
fc | The fold_compound the corrections should be bound to |
modification_sites | A list of modification site, i.e. positions that contain the modified base (1-based, last element in the list indicated by 0) |
options | A bitvector of options how to handle the input, e.g. VRNA_SC_MOD_DEFAULT |
options
= VRNA_SC_MOD_DEFAULT int vrna_sc_mod_inosine | ( | vrna_fold_compound_t * | fc, |
const unsigned int * | modification_sites, | ||
unsigned int | options | ||
) |
#include <ViennaRNA/constraints/soft_special.h>
Add soft constraint callbacks for Inosine.
This is a convenience wrapper to add support for inosine using the soft constraint callback mechanism. Modification sites are provided as a list of sequence positions (1-based). Energy parameter corrections are derived from [30] and [31].
fc | The fold_compound the corrections should be bound to |
modification_sites | A list of modification site, i.e. positions that contain the modified base (1-based, last element in the list indicated by 0) |
options | A bitvector of options how to handle the input, e.g. VRNA_SC_MOD_DEFAULT |
options
= VRNA_SC_MOD_DEFAULT int vrna_sc_mod_7DA | ( | vrna_fold_compound_t * | fc, |
const unsigned int * | modification_sites, | ||
unsigned int | options | ||
) |
#include <ViennaRNA/constraints/soft_special.h>
Add soft constraint callbacks for 7-deaza-adenosine (7DA)
This is a convenience wrapper to add support for 7-deaza-adenosine using the soft constraint callback mechanism. Modification sites are provided as a list of sequence positions (1-based). Energy parameter corrections are derived from [24].
fc | The fold_compound the corrections should be bound to |
modification_sites | A list of modification site, i.e. positions that contain the modified base (1-based, last element in the list indicated by 0) |
options | A bitvector of options how to handle the input, e.g. VRNA_SC_MOD_DEFAULT |
options
= VRNA_SC_MOD_DEFAULT int vrna_sc_mod_purine | ( | vrna_fold_compound_t * | fc, |
const unsigned int * | modification_sites, | ||
unsigned int | options | ||
) |
#include <ViennaRNA/constraints/soft_special.h>
Add soft constraint callbacks for Purine (a.k.a. nebularine)
This is a convenience wrapper to add support for Purine using the soft constraint callback mechanism. Modification sites are provided as a list of sequence positions (1-based). Energy parameter corrections are derived from [16].
fc | The fold_compound the corrections should be bound to |
modification_sites | A list of modification site, i.e. positions that contain the modified base (1-based, last element in the list indicated by 0) |
options | A bitvector of options how to handle the input, e.g. VRNA_SC_MOD_DEFAULT |
options
= VRNA_SC_MOD_DEFAULT int vrna_sc_mod_dihydrouridine | ( | vrna_fold_compound_t * | fc, |
const unsigned int * | modification_sites, | ||
unsigned int | options | ||
) |
#include <ViennaRNA/constraints/soft_special.h>
Add soft constraint callbacks for dihydrouridine.
This is a convenience wrapper to add support for dihydrouridine using the soft constraint callback mechanism. Modification sites are provided as a list of sequence positions (1-based). Energy parameter corrections are derived from Rosetta/RECESS predictions.
fc | The fold_compound the corrections should be bound to |
modification_sites | A list of modification site, i.e. positions that contain the modified base (1-based, last element in the list indicated by 0) |
options | A bitvector of options how to handle the input, e.g. VRNA_SC_MOD_DEFAULT |
options
= VRNA_SC_MOD_DEFAULT