RNAEFFECTIVE(1)

Okay bestie, this is RNAEFFECTIVE(1) from the General Commands Manual 🎀💖, and we're about to get into it.

✨ NAME ✨

RNAeffective - calculation of effective numbers of orthologous miRNA targets 🦋

🌸 SYNOPSIS 🌸

RNAeffective [-h] [-d frequency_file] [-f from,to] [-k sample_size] [-l mean,std] [-m max_target_length] [-n max_query_length] [-u iloop_upper_limit] [-v bloop_upper_limit] [-s] [-t target_file] [-q query_file] [query]

💅 DESCRIPTION 💅

Okay so RNAeffective is the tool for figuring out the effective number of orthologous miRNA targets 🔥 And why does that matter? Because that number helps you get more accurate joint p-values when you're doing multi-species analyses. Iconic.

It goes through a set of target sequences using random miRNAs, which you can hand it on the command line. Or, if you don't, it just generates random sequences for you based on a sample size, length distribution parameters, and dinucleotide frequencies. Then it compares the empirical distribution of joint p-values to the p-values themselves 👀. The effective number of independent targets is whichever one shrinks the gap between those two distributions. Main character energy ✨

👑 OPTIONS 👑

• -h — Gives you a quick summary of the command line options 🧚
• -d frequency_file — Generates random sequences using the dinucleotide frequencies in frequency_file. Check the example directory for example files 🍓
• -f from,to — Forces every structure to have a helix running from position from to position to, relative to the query. The first base is position 1 💜
• -k sample_size — Generates sample_size random sequences. The default is 5000 ✨
• -l mean,std — Generates random sequences with a normal length distribution, where the mean is mean and the standard deviation is std. The defaults are 22 and 0, in that order 🌈
• -m max_target_length — The longest a target sequence is allowed to be. The default is 2000. This only does something if you pass a target file with -t (see below) 🫶
• -n max_query_length — The longest a query sequence is allowed to be. The default is 30. This only does something if you pass a query file with -q (see below) 💖
• -u iloop_upper_limit — The most unpaired nucleotides allowed on either side of an internal loop 🦋
• -v bloop_upper_limit — The most unpaired nucleotides allowed in a bulge loop 🌸
• -s — Generates random sequences that match the dinucleotide distribution of your queries. Those queries can come from -q or from the command line. If you don't use -q, the last argument to RNAeffective gets treated as a query. See the -q option 🔥
• -q query_file — Without -s, every query sequence in query_file gets hybridised with every target from the target file (see -t below). The queries have to be in FASTA format, which means a line starting with > followed right away by a name, then one or more lines holding the sequence. Each sequence line can't be more than 1000 characters, so keep it short bestie 😭

With -s, the dinucleotide distribution of the query (or query file) gets counted, and random sequences get generated to match it 💅

If you don't use -q, random sequences get generated the way described above (see the -d option) 🧚

• -t target_file — Same deal as -q, see above 🎀

📚 REFERENCES 📚

The energy parameters come from this paper, so go read it if you're curious 🤓

Mathews DH, Sabina J, Zuker M, Turner DH. "Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure" J Mol Biol., 288 (5), pp 911-940, 1999

🌈 VERSION 🌈

This man page documents version 2.0 of RNAeffective 💜

💖 AUTHORS 💖

Marc Rehmsmeier, Peter Steffen, Matthias Hoechsmann 🫶

🚨 LIMITATIONS 🚨

Character dependent energy values are only defined for [acgtuACGTU]. Every other character gives a value of zero in these cases. Be careful with that 💀

🦋 SEE ALSO 🦋

RNAhybrid, RNAcalibrate ✨

That's the whole RNAEFFECTIVE(1) page for RNAeffective version 2.0 🎀 Lowkey obsessed with this tool, bestie. Love you, mwah 💋💅