NCOILS(1)

📦
version 2002 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

🌸 NCOILS 💖

okay bestie, welcome to ncoils from the fine folks in User Commands — this is the little program that looks at your protein sequence and is like "hmm, is this giving coiled-coil energy?" and honestly? it ate. 💅

✨ NAME ✨

ncoils — prediction of coiled-coil secondary structure elements. that's it, that's the whole vibe. 🧬🦋

🎀 SYNOPSIS 🎀

ncoils [OPTION] < [FASTA FILE]
ncoils -f < /usr/share/doc/ncoils/1srya.fa

like. you just pipe your FASTA file in and she does her thing. main character behavior fr fr. 👑

🌈 DESCRIPTION 🌈

so ncoils is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. that's the whole first step, no cap.

then — and this is the iconic part — by comparing this score to the distribution of scores in globular and coiled-coil proteins, the program calculates the probability that your sequence will adopt a coiled-coil conformation. it's literally a vibe check but for protein structure. 🔥

💅 OPTIONS 💅

  • -f, -fasta — fasta output. coils show up as 'x', just like '-x' in seg. so cute, so readable. ✨
  • -c — concise mode, aka the "just tell me the tea" mode: which sequences have any coils (and how many). 🫶
  • -min_seg <int> — for concise mode. only report a sequence if it has >= min coil segments. no filler, only real ones. 💀
  • -min_P <float> — minimum P to define a coil segment. DEFAULT = 0.5. 🎯
  • -win <int> — window size. DEFAULT = 21. 🪟
  • -w — weight heptad positions a&d the same as b,c,e,f,g. equal treatment for everybody, we love to see it. ⚖️
  • -v — verbose/debug mode. print extra junk. (affectionate. it IS junk. she said so herself.) 🙈

🍓 EXAMPLES 🍓

first one, and yes it's calling coils-wrap — that's what the page says, i don't make the rules bestie:

coils-wrap -m MTIDK -i /usr/share/doc/ncoils/1srya.fa -o /tmp/coils.out
-r /tmp/coils_raw.txt && less /tmp/coils.out /tmp/coils_raw.txt

and then the lil snack-sized one:

ncoils -win 14 < /usr/share/doc/ncoils/1srya.fa

🧚 ENVIRONMENT 🧚

  • COILSDIR — specifies the directory containing the file new.mat, overriding the default /usr/share/ncoils. so if your matrices live somewhere else, this is how you tell her. 💜

⭐ FILES ⭐

  • /usr/share/ncoils/*.mat — matrix data files. the secret sauce. 🫙

👑 AUTHOR 👑

R.B. Russell, A.N. Lupas — legends, honestly.

GPL. free as in slay. 🎀

Based on Lupas, Van Dyck & Stock (1991) Science 252,1162-1164.

🔥 SEE ALSO 🔥

plus the reading list, because she's well-read:

  • A Lupas: Prediction and Analysis of Coiled-Coil Structures. Methods in Enzymology, 266, 513-525, 1996
  • A. Lupas, M. Van Dyke, and J. Stock: Predicting coiled coils from protein sequences. Science, 252, 1162-1164, 1991
okay that's the whole page bestie, every flag, every default, every path, all of it. go predict some coils. i'm obsessed. 😭✨

this was ncoils, manual page, version 2002, dated 2021-08-15. mwah. 💋

📦 where this page comes from