RNAHEAT(1)

📦
version 2.7.0 · 5 versions
, in ubuntu resolute, ubuntu stonking

🎀 Hey Bestie, Welcome to RNAheat 🎀

Okay so this is the RNAHEAT(1) page, filed under User Commands, and it's all about RNAheat 2.7.0 🧬 It's a command-line tool and it is literally so good at what it does. Let's get into it 💅

✨ NAME ✨

RNAheat is the manual page for RNAheat 2.7.0 🌸

✨ SYNOPSIS ✨

RNAheat [OPTIONS] [<input0>] [<input1>]...

✨ DESCRIPTION ✨

RNAheat 2.7.0 is the main character here 👑 It calculates the specific heat of RNAs 🔥

So basically, it reads RNA sequences from stdin or from input files, then works out their specific heat across a temperature range from t1 to t2. It gets this from the partition function using numeric differentiation, which is giving math realness 🤓 The results get printed to stdout as pairs of temperature in C and specific heat in kcal/(mol*K) 🦋

It keeps reading new sequences until it hits a line that's just the single character @, or until it reaches end of file 🫶

  • -h, --help — Prints help and exits 🌷
  • --detailed-help — Prints help including all the details and hidden options, then exits 🔍
  • --full-help — Prints help including hidden options, then exits ✨
  • -V, --version — Prints the version and exits 🎀
  • -v, --verbose — Gets chatty 💬 (default=off). It lowers the log level setting so even INFO messages get passed through, which is so extra but in a good way 🌈

💌 I/O Options

Command line options for input and output (pre-)processing. These are your input and output glow-up 💖

  • -i, --infile=filename — Reads a file instead of reading from stdin 📂 By default, RNAheat reads input from stdin or from the file(s) that come after the RNAheat command. With this one you can name the input files that data gets read from. Heads up, any extra files you pass to RNAheat still get processed too 🙈
  • -j, --jobs[=number] — Splits batch input into jobs and runs them in parallel using multiple threads 🧵 A value of 0 means it uses as many parallel threads as there are computation cores (default=0). Normally input gets processed one sequence at a time, but with this switch you can process lots of sequences at once ⚡ RNAheat makes as many parallel computation slots as you ask for and hands out the input sequences from your file(s) to whichever slots are free. Just know this uses more memory 💀, because input alignments have to stay in memory until a slot opens up, and each running job needs its own dynamic programming matrices.
  • --unordered — Doesn't try to keep the output in the same order as the input while parallel processing is happening (default=off) 🙃 When parallel processing (the --jobs flag) is on, the order things get processed in depends on the host machine's job scheduler. So the output to stdout or to files will most likely NOT match the order of the input data. By default RNAheat uses a special data structure to keep results in order, but that costs memory, since everything has to be held onto until chunks of consecutive, ordered output are ready. Set this flag and RNAheat stops buffering and prints each result as soon as it's computed 🚀
  • --noconv — Stops RNAheat from automatically swapping nucleotide T for U (default=off) 🧬
  • --auto-id — Automatically generates an ID for each sequence (default=off) 🪪 By default RNAheat pulls an ID out of the input sequence data when the input file format allows it. Sequence IDs usually live in the FASTA header of input sequences. With this flag on, RNAheat ignores any IDs from the input and generates one for each sequence instead. Each ID is a prefix plus an increasing number. You can also use this flag to add a FASTA header to the output even when the input doesn't have one ✨
  • --id-prefix=STRING — Sets the prefix for automatically generated IDs (as used in output file names) (default=sequence) 🏷️ When this is set, each sequence's FASTA id gets prefixed with your string, so the ids look like >prefix_xxxx, where xxxx is the sequence number. Note: setting this parameter implies --auto-id.
  • --id-delim=CHAR — Changes the delimiter between the prefix and the increasing number for automatically generated IDs (as used in output file names) (default=_) 🖍️ It swaps out the default _ that sits between the prefix string and the number.
  • --id-digits=INT — Sets how many digits the counter has in automatically generated alignment IDs (default=4) 🔢 Generated alignment IDs start at 1 and get left-padded with zeros so the number is always the same width. This option lets you pick that width however you like. We allow numbers in the range [1:18]. This option implies --auto-id.
  • --id-start=LONG — Sets the first number in automatically generated alignment IDs (default=1) 🥇 Generated sequence IDs usually start at 1, but with this you can start wherever you want. Note: negative numbers are not allowed. Note: setting this parameter means any IDs from the input data get ignored, so it turns on the --auto-id flag.
  • --log-level=level — Sets the log level threshold (default=2) 📊 By default, log messages are filtered so only warnings (level 2) or errors (level 3) get printed. Higher values mean fewer messages. Log level 5 turns off all messages, even errors and other critical stuff 🤫
  • --log-file[=filename] — Prints log messages to a file instead of stderr (default=RNAheat.log) 📝
  • --log-time — Adds a time stamp to log messages (default=off) ⏰
  • --log-call — Includes the file and line of the log calling function (default=off) 🕵️‍♀️

🧪 Algorithms

Select additional algorithms which should be included in the calculations. Bestie, this is where the science gets spicy 🌶️

  • --Tmin=t1 — Sets the lowest temperature (default=0) 🥶
  • --Tmax=t2 — Sets the highest temperature (default=100) 🥵
  • --stepsize=FLOAT — Calculates the partition function every stepsize degrees C (default=1.) 📏
  • -m, --ipoints=ipoints — RNAheat fits a parabola to 2*ipoints+1 data points to calculate 2nd derivatives 📈 Turning this up gives you a smoother curve (default=2) 🧈
  • -c, --circ — Assumes a circular RNA molecule instead of a linear one (default=off) 💍
  • -g, --gquad — Incorporates G-Quadruplex formation into the structure prediction algorithm (default=off) 🌀

🎯 Structure Constraints

Command line options to interact with the structure constraints feature of this program. Constraints keep things in check, periodt 🙌

  • --maxBPspan=INT — Sets the maximum base pair span (default=-1) 📐

⚡ Energy Parameters

Energy parameter sets can be adapted or loaded from user-provided input files 🔋

  • -P, --paramFile=paramfile — Reads energy parameters from paramfile instead of using the default parameter set 💾 Different sets of energy parameters for RNA and DNA should come with your distribution. Check the RNAlib documentation for the details on the file format. The placeholder file name DNA can be used to load DNA parameters without actually specifying any input file, which is such a time-saver 🧚
  • -4, --noTetra — Skips the special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins (default=off) 🙅‍♀️ This one is mostly for testing 🧪
  • --salt=DOUBLE — Sets the salt concentration in molar (M). The default is 1.021M 🧂

✨ REFERENCES ✨

Okay so if you use this program in your work, you need to cite these papers, bestie 📚💅

Citations you should know:

  • R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler and I.L. Hofacker (2011), "ViennaRNA Package 2.0", Algorithms for Molecular Biology: 6:26 🦋
  • I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994), "Fast Folding and Comparison of RNA Secondary Structures", Monatshefte f. Chemie: 125, pp 167-188 🌸
  • R. Lorenz, I.L. Hofacker, P.F. Stadler (2016), "RNA folding with hard and soft constraints", Algorithms for Molecular Biology 11:1 pp 1-13 ✨

The energy parameters are taken from these two bangers 🔥:

  • D.H. Mathews, M.D. Disney, D. Matthew, J.L. Childs, S.J. Schroeder, J. Susan, M. Zuker, D.H. Turner (2004), "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure", Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292 💜
  • D.H Turner, D.H. Mathews (2009), "NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure", Nucleic Acids Research: 38, pp 280-282 🧚

✨ AUTHOR ✨

The squad who built this is Ivo L Hofacker, Peter F Stadler, Ronny Lorenz 🫶👑

✨ REPORTING BUGS ✨

Okay, real talk: if you think the output looks wrong, our program is probably right and nature is the one being sus 💀🙈

If in doubt our program is right, nature is at fault.

Got comments? Send them to rna@tbi.univie.ac.at 💌

✨ SEE ALSO ✨

  • RNAfold(1) — the sister page you'll want next, main character energy 🧚⭐

Okay that's the whole thing, bestie! You just read the second half of the RNAheat 2.7.0 manual, dated February 2026, with the RNAHEAT(1) page name 🌈💖 Stay iconic and go cite those papers 💅✨

📦 where this page comes from