RNALOCMIN(1)

✨ NAME ✨

okay bestie, welcome to the RNAlocmin manual page 💖 this one is for RNAlocmin 2.1.0, and it's a User Commands page 🎀

RNAlocmin - manual page for RNAlocmin 2.1.0

📜 SYNOPSIS 📜

RNAlocmin [OPTIONS]... [FILES]...

💅 DESCRIPTION 💅

RNAlocmin 2.1.0, obviously 🫶

Calculate local minima from structures via gradient walks. Example usage:

RNAsubopt -p 10000 < "sequence.txt" > "suboptp.txt" RNAlocmin -s "sequence.txt" [OPTIONS] < "suboptp.txt"

• -h, --help — Print help and exit 🌷
• --detailed-help — Print help, including all details and hidden options, and exit 🔍
• --full-help — Print help, including hidden options, and exit
• -V, --version — Print version and exit ✨

🌸 General options 🌸

• -s, --seq=STRING — Your sequence file, in FASTA format 🧬 If the sequence is already the first line of the input file, you can skip this one. default=`seq.txt'
• -p, --previous=STRING — Feed in previously found LM (the output from RNAlocmin or barriers). If you use this, you don't need --seq 💅
• -m, --move=STRING — Pick your move set. I ==> insertion & deletion of base pairs. S ==> I&D& switch of base pairs. Possible values: "I", "S". default=`I'
• -n, --min-num=INT — Max number of local minima returned. 0 means unlimited. default=`100000'
• --find-num=INT — Max number of local minima to find. The default is unlimited, which means it crawls through the whole input file 🕷️
• -v, --verbose-lvl=INT — Level of verbosity: 0 = nothing, 4 = full. default=`0'

WARNING: higher verbose levels increase the computation time 😭

• --depth=INT — Depth of the findpath search. A higher value makes the running time go up linearly. default=`10'
• --minh=DOUBLE — Only print minima with an energy barrier greater than this one. default=`0.0'
• --minh-lite — When flooding with the --minh option, only search for saddles and skip looking for a lower LM. It's a tiny bit more efficient, but with it on, the results may omit some non-shallow minima, especially with a higher --minh value. (default=off)
• -w, --walk=STRING — Pick your walking method. D ==> gradient descent. F ==> use the first found lower energy structure. R ==> use a random lower energy structure. R doesn't work with --noLP or -m S. Possible values: "D", "F", "R". default=`D'
• --noLP — Work only with canonical RNA structures (no isolated base pairs). It can't be combined with the random walk (-w R) or the shift move set (-m S). (default=off)
• -e, --useEOS — Use the energy_of_structure_pt calculation instead of energy_of_move. It's slower, but it should not affect the results. (default=off)
• -P, --paramFile=STRING — Read energy parameters from a paramfile instead of using the default parameter set 📂
• -d, --dangles=INT — How to treat "dangling end" energies for bases next to helices in free ends and multi-loops. default=`2'
  • -d1: only unpaired bases can participate in at most one dangling end. This is the default for mfe folding, but it's unsupported for partition function folding.
  • -d2: this check is ignored, and dangling energies get added for bases next to a helix on both sides no matter what. This is the default for partition function folding (-p). -d0 ignores dangling ends altogether (mostly for debugging).
  • -d3: mfe folding will allow coaxial stacking of adjacent helices in multi-loops. Right now it won't allow coaxial stacking of the two interior pairs in a loop of degree 3, and it only works for mfe folding.
  • Note that by default (as well as with -d1 and -d3), pf and mfe folding treat dangling ends differently. Use -d2 in addition to -p to make sure both algorithms use the same energy model 🫶
• --fix-barriers=STRING — Fix the barrier file for interior loops (it just recomputes if all LM in the barrier output are LM). If you specify this, you don't need --previous or --seq 🔧
• -k, --pseudoknots — Allow pseudoknots according to the "gfold" model. H, K, L, and M types (genus one) of pseudoknots are allowed. This increases computation time greatly. It can't be combined with the shift move set (-m S). (default=off)
• --just-read — Don't expect input from stdin, just do postprocessing. (default=off)
• -N, --neighborhood — Use the Neighborhood routines to perform gradient descent. It can't be combined with the shift move set (-m S) or pseudoknots (-k). It's a test option 🧪 (default=off)
• --degeneracy-off — Don't deal with degeneracy. Just select the lexicographically first one from the same-energy neighbors. (default=off)
• --just-output — Don't store the minima and optimize. Just compute the minima directly and output them. The output file can contain duplicates. (default=off)

🎀 Barrier tree 🎀

• -b, --bartree — Generate an approximate barrier tree. (default=off)
• --barr-name=STRING — Name of the barrier tree output file. Using this switches on the -b flag. default=`treeRNAloc.ps'

🦋 Kinetics (rates for treekin program) 🦋

• --barrier-file=STRING — File for saddle heights between LM. It simulates the output format of the barriers program.
• -r, --rates — Create rates for treekin. (default=off)
• -f, --rates-file=STRING — File where the rates get written. Using this switches on the -r flag. default=`rates.out'
• -T, --temp=DOUBLE — Temperature in Celsius (only for rates). default=`37.0'

🌈 Flooding parameters (flooding occurs only with -r, -b, or --minh option) 🌈

• --floodPortion=DOUBLE — Fraction of minima to flood. It floods the first minima that have a low number of inwalking sample structures. 0.0 means no flood, and 1.0 means try to flood all. Only usable with -r or -b. default=`0.95'
• --floodMax=INT — Flood cap: how many structures to flood in one basin. default=`1000'

🍓 Miscelaneous 🍓

• --numIntervals=INT — Number of intervals for Jing's visualisation. default=`0'
• --eRange=FLOAT — Only report LM whose energy is in the range <MFE (or lowest found LM), MFE+eRange>, measured in kcal/mol. 🌡️
• --allegiance=STRING — Filename where the allegiance of structures gets output. It only works properly with RNAsubopt -e list. 💜

That's the whole page, bestie! 🧚 You're officially RNAlocmin 2.1.0 literate, from July 2017 on the RNALOCMIN(1) manual 💖✨