|
|
ovrnaheat |
Please help by correcting and extending the Wiki pages.
This is a port of the Vienna RNA package program RNAheat.
It reads RNA sequences and calculates their specific heat in the temperature range t1 to t2, from the partition function by numeric differentiation. The result is output as a list of pairs of temperature in C and specific heat in Kcal/(Mol*K).
The program will continue to read new sequences until a line consisting of the single character "@" or an end of file condition is encountered.
See the original documentation for the Vienna RNA package http://www.tbi.univie.ac.at/~ivo/RNA/
% ovrnaheat -mintemp 30 -maxtemp 120 -step 0.1 -smoothing 4 Calculate specific heat of RNA melting Input nucleotide sequence: cofold-red.fasta Vienna RNAfold output file [red.ovrnaheat]: |
Go to the input files for this example
Go to the output files for this example
Calculate specific heat of RNA melting
Version: EMBOSS:6.5.0.0
Standard (Mandatory) qualifiers:
[-sequence] sequence Nucleotide sequence filename and optional
format, or reference (input USA)
[-outfile] outfile [*.ovrnaheat] Vienna RNAfold output file
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-paramfile infile Vienna RNA parameters file (optional)
-mintemp float [0.0] Temperature (Any numeric value)
-maxtemp float [100.0] Temperature (Any numeric value)
-[no]gu boolean [Y] Allow GU pairs
-[no]closegu boolean [Y] Allow GU pairs at end of helices
-[no]lp boolean [Y] Allow lonely pairs
-[no]convert boolean [Y] Convert T to U
-nsbases string Non-standard bases (Any string)
-[no]tetraloop boolean [Y] Stabilizing energies for tetra-loops
-energy menu [0] Rarely used option to fold sequences
from the ABCD... alphabet (Values: 0 (BP); 1
(Any with GC); 2 (Any with AU parameters))
-smoothing integer [2] Parabola fitting value (Any integer
value)
-step float [1.0] Step size in degrees C (Number from
0.010 to 1000.000)
-dangles menu [2] Method (Values: 0 (Ignore); 2 (Always
use dangling energies))
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of the sequence to be used
-send1 integer End of the sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-scircular1 boolean Sequence is circular
-sformat1 string Input sequence format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-outfile" associated qualifiers
-odirectory2 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit
|
| Qualifier | Type | Description | Allowed values | Default | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||
| [-sequence] (Parameter 1) |
sequence | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required | ||||||
| [-outfile] (Parameter 2) |
outfile | Vienna RNAfold output file | Output file | <*>.ovrnaheat | ||||||
| Additional (Optional) qualifiers | ||||||||||
| (none) | ||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||
| -paramfile | infile | Vienna RNA parameters file (optional) | Input file | Required | ||||||
| -mintemp | float | Temperature | Any numeric value | 0.0 | ||||||
| -maxtemp | float | Temperature | Any numeric value | 100.0 | ||||||
| -[no]gu | boolean | Allow GU pairs | Boolean value Yes/No | Yes | ||||||
| -[no]closegu | boolean | Allow GU pairs at end of helices | Boolean value Yes/No | Yes | ||||||
| -[no]lp | boolean | Allow lonely pairs | Boolean value Yes/No | Yes | ||||||
| -[no]convert | boolean | Convert T to U | Boolean value Yes/No | Yes | ||||||
| -nsbases | string | Non-standard bases | Any string | |||||||
| -[no]tetraloop | boolean | Stabilizing energies for tetra-loops | Boolean value Yes/No | Yes | ||||||
| -energy | list | Rarely used option to fold sequences from the ABCD... alphabet |
|
0 | ||||||
| -smoothing | integer | Parabola fitting value | Any integer value | 2 | ||||||
| -step | float | Step size in degrees C | Number from 0.010 to 1000.000 | 1.0 | ||||||
| -dangles | list | Method |
|
2 | ||||||
| Associated qualifiers | ||||||||||
| "-sequence" associated sequence qualifiers | ||||||||||
| -sbegin1 -sbegin_sequence |
integer | Start of the sequence to be used | Any integer value | 0 | ||||||
| -send1 -send_sequence |
integer | End of the sequence to be used | Any integer value | 0 | ||||||
| -sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||
| -sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||
| -snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||
| -sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N | ||||||
| -slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N | ||||||
| -supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N | ||||||
| -scircular1 -scircular_sequence |
boolean | Sequence is circular | Boolean value Yes/No | N | ||||||
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |||||||
| -iquery1 -iquery_sequence |
string | Input query fields or ID list | Any string | |||||||
| -ioffset1 -ioffset_sequence |
integer | Input start position offset | Any integer value | 0 | ||||||
| -sdbname1 -sdbname_sequence |
string | Database name | Any string | |||||||
| -sid1 -sid_sequence |
string | Entryname | Any string | |||||||
| -ufo1 -ufo_sequence |
string | UFO features | Any string | |||||||
| -fformat1 -fformat_sequence |
string | Features format | Any string | |||||||
| -fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |||||||
| "-outfile" associated outfile qualifiers | ||||||||||
| -odirectory2 -odirectory_outfile |
string | Output directory | Any string | |||||||
| General qualifiers | ||||||||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||
| -error | boolean | Report errors | Boolean value Yes/No | Y | ||||||
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | ||||||
>red AUGAAGAUGA |
30.0 0.0249226 30.1 0.0246153 30.2 0.0243077 30.3 0.0240077 30.4 0.0237102 30.5 0.0234176 30.6 0.0231288 30.7 0.022845 30.8 0.0225598 30.9 0.0222795 31.0 0.0220043 31.1 0.0217381 31.2 0.0214691 31.3 0.0212051 31.4 0.0209456 31.5 0.0206852 31.6 0.0204331 31.7 0.0201802 31.8 0.0199351 31.9 0.0196904 32.0 0.0194501 32.1 0.0192143 32.2 0.0189796 32.3 0.0187481 32.4 0.0185177 32.5 0.0182931 32.6 0.0180723 32.7 0.0178506 32.8 0.0176348 32.9 0.0174194 33.0 0.0172098 33.1 0.0170001 33.2 0.0167962 33.3 0.0165928 33.4 0.0163919 33.5 0.0161935 33.6 0.0159983 33.7 0.0158062 33.8 0.015616 33.9 0.0154289 34.0 0.0152444 34.1 0.0150598 34.2 0.014879 34.3 0.0147013 34.4 0.0145256 34.5 0.0143517 34.6 0.0141817 34.7 0.0140109 34.8 0.0138439 34.9 0.0136775 [Part of this file has been deleted for brevity] 114.9 2.13815e-05 115.0 2.12305e-05 115.1 2.1236e-05 115.2 2.10849e-05 115.3 2.09859e-05 115.4 2.09391e-05 115.5 2.08923e-05 115.6 2.07932e-05 115.7 2.07462e-05 115.8 2.05948e-05 115.9 2.04955e-05 116.0 2.03962e-05 116.1 2.03491e-05 116.2 2.01973e-05 116.3 2.01502e-05 116.4 2.01554e-05 116.5 2.01605e-05 116.6 2.00086e-05 116.7 1.99613e-05 116.8 1.98092e-05 116.9 1.97619e-05 117.0 1.96621e-05 117.1 1.96147e-05 117.2 1.95148e-05 117.3 1.93624e-05 117.4 1.93148e-05 117.5 1.93198e-05 117.6 1.92197e-05 117.7 1.90671e-05 117.8 1.91245e-05 117.9 1.89717e-05 118.0 1.88189e-05 118.1 1.87711e-05 118.2 1.87233e-05 118.3 1.86755e-05 118.4 1.8575e-05 118.5 1.84745e-05 118.6 1.84265e-05 118.7 1.83786e-05 118.8 1.82779e-05 118.9 1.81772e-05 119.0 1.81819e-05 119.1 1.80811e-05 119.2 1.79275e-05 119.3 1.79848e-05 119.4 1.78311e-05 119.5 1.78357e-05 119.6 1.76819e-05 119.7 1.76336e-05 119.8 1.75324e-05 119.9 1.74313e-05 |
| Program name | Description |
|---|---|
| banana | Plot bending and curvature data for B-DNA |
| btwisted | Calculate the twisting in a B-DNA sequence |
| einverted | Find inverted repeats in nucleotide sequences |
| ovrnaalifold | Calculate secondary structures for a set of aligned RNAs |
| ovrnaalifoldpf | Calculate secondary structures for a set of aligned RNAs (partition) |
| ovrnacofold | Calculate secondary structures of RNA dimers |
| ovrnacofoldconc | Calculate secondary structures of RNA dimers (concentrations) |
| ovrnacofoldpf | Calculate secondary structures of RNA dimers (partitioning) |
| ovrnadistance | Calculate distances between RNA secondary structures |
| ovrnaduplex | Predict RNA duplex (hybridization) sites and structure |
| ovrnaeval | Calculate energy of RNA sequences with a given secondary structure |
| ovrnaevalpair | Calculate energy of RNA sequences on given secondary structure |
| ovrnafold | Calculate min. energy RNA structure / pair probabilities (partition) |
| ovrnafoldpf | Calculate min. energy RNA structure / pair probabilities |
| ovrnainverse | Find RNA sequences with a given secondary structure |
| ovrnalfold | Calculate locally stable secondary structures of RNAs |
| ovrnaplot | Draw RNA secondary structures |
| ovrnasubopt | Calculate suboptimal secondary structure of RNA |
| sirna | Find siRNA duplexes in mRNA |
| vrna2dfold | Calculate RNA structures and samples of k,l neighbourhoods |
| vrnaaliduplex | RNA duplex calculation for two sequence alignments |
| vrnaalifold | Calculate secondary structures for a set of aligned RNAs |
| vrnaalifoldpf | Calculate secondary structures for a set of aligned RNAs (partition) |
| vrnacofold | Calculate secondary structures of RNA dimers |
| vrnacofoldconc | Calculate secondary structures of RNA dimers (concentrations) |
| vrnacofoldpf | Calculate secondary structures of RNA dimers (partitioning) |
| vrnadistance | Calculate distances between RNA secondary structures |
| vrnaduplex | Predict RNA duplex (hybridization) sites and structure |
| vrnaeval | Calculate energy of RNA sequences with a given secondary structure |
| vrnaevalpair | Calculate energy of RNA sequences on given secondary structure |
| vrnafold | Calculate min. energy RNA secondary structures and pair probabilities |
| vrnafoldpf | Calculate min. energy RNA structures / pair probabilities (partition) |
| vrnaheat | Calculate specific heat of RNA melting |
| vrnainverse | Find RNA sequences with a given secondary structure |
| vrnalalifoldpf | Calculate secondary structures for a set of aligned RNAs (partition) |
| vrnalfold | Calculate locally stable secondary structures of RNAs |
| vrnalfoldz | Calculate locally stable secondary structures of RNAs plus zscore |
| vrnapkplex | Calculate RNA structures plus pseudoknots |
| vrnaplfold | Compute avg. pair probabilities for local base pairs in RNA sequences |
| vrnaplot | Draw RNA secondary structures |
| vrnasubopt | Calculate suboptimal secondary structures of RNAs |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.