DAN(1e)

📦 version 6.6.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 DAN(1e) — the melting temperature girlie 💖

okay so bestie, you found the page for dan, straight out of the EMBOSS Manual for Debian. pull up a chair, grab a boba, and let's get into it 🧋✨

✨ NAME ✨

dan — calculates nucleic acid melting temperature 🔥🧬

✨ SYNOPSIS ✨

dan -sequence seqall -windowsize integer -shiftincrement integer
    -dnaconc float -saltconc float [-product toggle] -formamide float
    -mismatch float -prodlen integer [-thermo toggle] -temperature float
    -rna boolean -plot toggle -mintemp float -graph xygraph
    -outfile report

dan -help

like, that's the whole vibe. every flag, no notes 💅

✨ DESCRIPTION ✨

dan is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). fr fr, it lives in the "Nucleic:Properties,Nucleic:Composition" command group(s). she's a properties girlie AND a composition girlie, we love a multitasker 👑

✨ OPTIONS ✨

🌸 Input section 🌸

  • -sequence seqall — this is your input sequence, bestie. no description beyond that, she just takes it 🫶

🌸 Required section 🌸

okay so these ones aren't optional, you literally cannot skip them, periodt.

  • -windowsize integer — the values of melting point and other thermodynamic properties of the sequence are determined by taking a short length of sequence known as a window and determining the properties of the sequence in that window. the window is incrementally moved along the sequence with the properties being calculated at each new position. Default value: 20 🪟
  • -shiftincrement integer — this is the amount by which the window is moved at each increment in order to find the melting point and other properties along the sequence. Default value: 1 👟
  • -dnaconc float — Default value: 50. 🧪
  • -saltconc float — Default value: 50. 🧂

🌸 Additional section 🌸

🎀 Product options 🎀

  • -product toggle — this prompts for percent formamide, percent of mismatches allowed and product length. it's giving "one toggle, three follow-up questions" energy 💬
  • -formamide float — this specifies the percent formamide to be used in calculations (it is ignored unless -product is used). Default value: 0.
  • -mismatch float — this specifies the percent mismatch to be used in calculations (it is ignored unless -product is used). Default value: 0.
  • -prodlen integer — this specifies the product length to be used in calculations (it is ignored unless -product is used). Default value: $(windowsize) — yes bestie, it literally inherits from your window size, she's connected like that 🔗

🎀 Thermodynamic options 🎀

  • -thermo toggle — output the DeltaG, DeltaH and DeltaS values of the sequence windows to the output data file. the trio ate, ngl 🌡️
  • -temperature float — if -thermo has been specified then this specifies the temperature at which to calculate the DeltaG, DeltaH and DeltaS values. Default value: 25. 🔥

🌸 Advanced section 🌸

  • -rna boolean — this specifies that the sequence is an RNA sequence and not a DNA sequence. choose your fighter 🥊

🌸 Output section 🌸

  • -plot toggle — if this is not specified then the file of output data is produced, else a plot of the melting point along the sequence is produced. it's giving "data or glow-up, pick one" 📊 vs 📈
  • -mintemp float — enter a minimum value for the temperature scale (y-axis) of the plot. Default value: 55. 📉
  • -graph xygraph — no extra notes on this one, she's just here doing her thing 🦋
  • -outfile report — if a plot is not being produced then data on the melting point etc. in each window along the sequence is output to the file. 📄✨

🐛 BUGS 🐛

found a bug? no stress, bestie. bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). they wanna hear from you fr fr 🙈💌

👀 SEE ALSO 👀

dan is fully documented via the tfm(1) system. iykyk 📚

👑 AUTHOR 👑

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

  • wrote the script used to autogenerate this manual page. iconic behaviour, honestly 🫡

this manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. it can be redistributed under the same terms as EMBOSS itself. 🎀

ok that's the whole page, you're officially a dan expert now, no cap 💅

EMBOSS version 6.4.0, dated 05/11/2012 — and that's the sign-off bestie, mwah, go melt some nucleic acids 🌈⭐💖

📦 where this page comes from