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vrnaheat |
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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/
% vrnaheat -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.vrnaheat]: |
Go to the input files for this example
Go to the output files for this example
Calculate specific heat of RNA melting
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-sequence] sequence Nucleotide sequence filename and optional
format, or reference (input USA)
[-outfile] outfile [*.vrnaheat] 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
-squick1 boolean Read id and sequence only
-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 | <*>.vrnaheat | ||||||
| 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 | ||||||
| -squick1 -squick_sequence |
boolean | Read id and sequence only | 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 0.013999 30.1 0.0139019 30.2 0.0138126 30.3 0.013718 30.4 0.0136311 30.5 0.013539 30.6 0.0134494 30.7 0.0133571 30.8 0.0132726 30.9 0.0131854 31 0.0130982 31.1 0.0130109 31.2 0.0129236 31.3 0.0128388 31.4 0.0127566 31.5 0.0126743 31.6 0.0125867 31.7 0.0125096 31.8 0.0124245 31.9 0.012342 32 0.0122647 32.1 0.0121794 32.2 0.0120994 32.3 0.0120219 32.4 0.0119417 32.5 0.0118668 32.6 0.0117865 32.7 0.0117114 32.8 0.0116363 32.9 0.0115585 33 0.0114833 33.1 0.0114107 33.2 0.0113327 33.3 0.01126 33.4 0.0111859 33.5 0.0111104 33.6 0.0110375 33.7 0.0109712 33.8 0.0108969 33.9 0.0108291 34 0.0107573 34.1 0.0106869 34.2 0.0106163 34.3 0.010551 34.4 0.0104817 34.5 0.0104123 34.6 0.0103469 34.7 0.0102801 34.8 0.0102133 34.9 0.0101477 [Part of this file has been deleted for brevity] 114.9 0.000651667 115 0.000656008 115.1 0.00066536 115.2 0.000672212 115.3 0.000678232 115.4 0.000682584 115.5 0.000687773 115.6 0.000693802 115.7 0.000699833 115.8 0.000705867 115.9 0.000711068 116 0.000715435 116.1 0.000722314 116.2 0.000723337 116.3 0.000729385 116.4 0.000734598 116.5 0.000738976 116.6 0.000741679 116.7 0.000748576 116.8 0.000752122 116.9 0.00075567 117 0.000757541 117.1 0.00076277 117.2 0.000765484 117.3 0.000768198 117.4 0.000770075 117.5 0.000773632 117.6 0.000778031 117.7 0.000779911 117.8 0.000782632 117.9 0.000785355 118 0.000787238 118.1 0.000788281 118.2 0.000789324 118.3 0.00079205 118.4 0.000794778 118.5 0.000795824 118.6 0.000796027 118.7 0.000797915 118.8 0.000799804 118.9 0.000802537 119 0.000802742 119.1 0.00080632 119.2 0.000809901 119.3 0.000812639 119.4 0.000816222 119.5 0.000819807 119.6 0.000821705 119.7 0.000827827 119.8 0.000828883 119.9 0.000832474 |
| Program name | Description |
|---|---|
| banana | Plot bending and curvature data for B-DNA |
| btwisted | Calculate the twisting in a B-DNA sequence |
| dan | Calculate nucleic acid melting temperature |
| 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 |
| ovrnaheat | Calculate specific heat of RNA melting |
| 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) |
| 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.