PRODIGAL(1)

💖 PRODIGAL(1) 💖

okay bestie, welcome to the User Commands corner of the manual, and today's main character is prodigal 🧬✨ she's the one and only, and she's about to find some genes for you. let's get into it.

✨ NAME ✨

prodigal — the microbial (bacterial and archaeal) gene finding program. yeah. that's her whole job. finding genes. slay. 👑

🌸 SYNOPSIS 🌸

prodigal [-a trans_file] [-c] [-d nuc_file] [-f output_type] [-g
tr_table] [-h] [-i input_file] [-m] [-n] [-o output_file] [-p mode] [-q]
[-s start_file] [-t training_file] [-v]

look at all those little flaggies. don't panic, we're gonna go through every single one, i promise. no flag left behind. 🫶

🦋 DESCRIPTION 🦋

okay so. Prodigal stands for Prokaryotic Dynamic Programming Genefinding Algorithm (yes, that's the actual name, and yes, it's giving very much academic baddie 💅). she's a microbial (bacterial and archaeal) gene finding program, and she was developed at Oak Ridge National Laboratory and the University of Tennessee. academic royalty fr fr. 🎀

💜 OPTIONS 💜

every single one, bestie. here we go.

• -a — write protein translations to the file you picked. proteins, but make it a file. 🍓
• -c — Closed ends. do NOT allow genes to run off the edges. keep them contained, keep them cozy, no gene escaping the party. 🙈
• -d — write the nucleotide sequences of the genes to the file you selected.
• -f — pick your output format: gbk, gff, or sco. default is gbk. choose your fighter. ⭐
• -g — specify which translation table to use. default is 11.
• -h — print the help menu and dip. that's it, that's the whole job. 👋
• -i — specify the input file. default reads from stdin. (so if you're a pipe girlie, you're covered. 😌)
• -m — treat runs of n's as masked sequence and do NOT build genes across them. respect the mask, bestie. 🎭
• -n — bypass the Shine-Dalgarno trainer and force the program to scan for motifs instead. (she'll just go looking by hand, essentially. iconic behaviour. 💅)
• -o — specify the output file. default writes to stdout.
• -p — select the procedure: single or meta. default is single.
• -q — run quietly. suppresses the normal stderr output. shhh. 🤫
• -s — write all the potential genes (with scores) to the file you selected. not just the winners, the whole audition tape. 🔥
• -t — write a training file (if none exists yet); otherwise, read and use the training file you specified. she learns, she remembers, she serves. 🧚
• -v — print the version number and exit. quick lil flex. ✨

heads up bestie: that synopsis means every one of these is optional — prodigal will happily do her thing with defaults if you just pipe her some sequence. no cap. 💖

and that's the whole page, gorgeous. this was prodigal 2.6.1, dated September 2014, and she's still out here finding genes like the queen she is. go read the rest of the manual, i'm obsessed with you, mwah 💋🌸🦋