General Options:

Below are command line options which alter the general behavior of this program

--Tmin=t1

Lowest temperature

(default=`0')

--Tmax=t2

Highest temperature

(default=`100')

--stepsize=FLOAT

Calculate partition function every stepsize degrees C

(default=`1.')

-m, --ipoints=ipoints

The program fits a parabola to 2*ipoints+1 data points to calculate 2nd derivatives. Increasing this parameter produces a smoother curve

(default=`2')

--noconv

Do not automatically substitude nucleotide "T" with "U"

(default=off)

-j, --jobs[=number]

Split batch input into jobs and start processing in parallel using multiple threads. A value of 0 indicates to use as many parallel threads as computation cores are available.

(default=`0')

Default processing of input data is performed in a serial fashion, i.e. one sequence at a time. Using this switch, a user can instead start the computation for many sequences in the input in parallel. RNAheat will create as many parallel computation slots as specified and assigns input sequences of the input file(s) to the available slots. Note, that this increases memory consumption since input alignments have to be kept in memory until an empty compute slot is available and each running job requires its own dynamic programming matrices.

--unordered

Do not try to keep output in order with input while parallel processing is in place.

(default=off)

When parallel input processing (--jobs flag) is enabled, the order in which input is processed depends on the host machines job scheduler. Therefore, any output to stdout or files generated by this program will most likely not follow the order of the corresponding input data set. The default of RNAheat is to use a specialized data structure to still keep the results output in order with the input data. However, this comes with a trade-off in terms of memory consumption, since all output must be kept in memory for as long as no chunks of consecutive, ordered output are available. By setting this flag, RNAheat will not buffer individual results but print them as soon as they have been computated.

-i, --infile=<filename>

Read a file instead of reading from stdin

The default behavior of RNAheat is to read input from stdin or the file(s) that follow(s) the RNAheat command. Using this parameter the user can specify input file names where data is read from. Note, that any additional files supplied to RNAheat are still processed as well.

--auto-id

Automatically generate an ID for each sequence. (default=off)

The default mode of RNAheat is to automatically determine an ID from the input sequence data if the input file format allows to do that. Sequence IDs are usually given in the FASTA header of input sequences. If this flag is active, RNAheat ignores any IDs retrieved from the input and automatically generates an ID for each sequence. This ID consists of a prefix and an increasing number. This flag can also be used to add a FASTA header to the output even if the input has none.

--id-prefix=prefix

Prefix for automatically generated IDs (as used in output file names)

(default=`sequence')

If this parameter is set, each sequences' FASTA id will be prefixed with the provided string. FASTA ids then take the form ">prefix_xxxx" where xxxx is the sequence number. Note: Setting this parameter implies --auto-id.

--id-delim=delimiter

Change the delimiter between prefix and increasing number for automatically generated IDs (as used in output file names)

(default=`_')

This parameter can be used to change the default delimiter "_" between

the prefix string and the increasing number for automatically generated ID.

--id-digits=INT

Specify the number of digits of the counter in automatically generated alignment IDs.

(default=`4')

When alignments IDs are automatically generated, they receive an increasing number, starting with 1. This number will always be left-padded by leading zeros, such that the number takes up a certain width. Using this parameter, the width can be specified to the users need. We allow numbers in the range [1:18]. This option implies --auto-id.

--id-start=LONG

Specify the first number in automatically generated alignment IDs.

(default=`1')

When sequence IDs are automatically generated, they receive an increasing number, usually starting with 1. Using this parameter, the first number can be specified to the users requirements. Note: negative numbers are not allowed. Note: Setting this parameter implies to ignore any IDs retrieved from the input data, i.e. it activates the --auto-id flag.

Structure Constraints:

Command line options to interact with the structure constraints feature of this program

--maxBPspan=INT

Set the maximum base pair span

(default=`-1')

Model Details:

-4, --noTetra

Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.

(default=off)

-d, --dangles=INT

How to treat "dangling end" energies for bases adjacent to helices in free ends and multi-loops

(default=`2')

With -d2 dangling energies will be added for the bases adjacent to a helix on both sides in any case

-d0 ignores dangling ends altogether (mostly for debugging).

--noLP

Produce structures without lonely pairs (helices of length 1).

(default=off)

For partition function folding this only disallows pairs that can only occur isolated. Other pairs may still occasionally occur as helices of length 1.

--noGU

Do not allow GU pairs

(default=off)

--noClosingGU

Do not allow GU pairs at the end of helices

(default=off)

-P, --paramFile=paramfile

Read energy parameters from paramfile, instead of using the default parameter set.

Different sets of energy parameters for RNA and DNA should accompany your distribution. See the RNAlib documentation for details on the file format. When passing the placeholder file name "DNA", DNA parameters are loaded without the need to actually specify any input file.

--nsp=STRING

Allow other pairs in addition to the usual AU,GC,and GU pairs.

Its argument is a comma separated list of additionally allowed pairs. If the first character is a "-" then AB will imply that AB and BA are allowed pairs. e.g. RNAheat -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy.

-e, --energyModel=INT

Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.

-g, --gquad

Incoorporate G-Quadruplex formation into the structure prediction algorithm.

(default=off)

-c, --circ

Assume a circular (instead of linear) RNA molecule.

(default=off)