TRANSDECODER.PREDICT(1)

📦
version 6.0.0 · 2 versions
, in ubuntu stonking

💖 NAME 💖

TransDecoder.Predict — predicts the likely coding regions among the ORFs

✨ DESCRIPTION ✨

okay bestie, so TransDecoder.Predict is the second half of the glow-up. It takes your ORFs and figures out which ones are actually the coding regions. 💅 And every time you run it, it greets you with this little banner, which is giving "I made this in my notes app at 3am but I'm also a genius":

       ########################################################################################
       #             ______                 ___                  __ #
       /_  __/______ ____ ___ / _ \___ _______  ___/ /__ ____ #             / /
       / __/ _ `/ _\(_-</ // / -_) __/ _ \/ _  / -_) __/ #            /_/ /_/
       \_,_/_//_/___/____/\__/\__/\___/\_,_/\__/_/   .Predict #
       ########################################################################################
       # #  Transdecoder.LongOrfs|http://transdecoder.github.io> -
       Transcriptome Protein Prediction # # #  Required: # #   -t <string>
       transcripts.fasta

The banner's also lowkey telling you this is all about Transcriptome Protein Prediction, and that it's the sibling of Transdecoder.LongOrfs over at http://transdecoder.github.io. 🦋

🌸 Required 🌸

You literally cannot run this without one thing, no cap:

  • -t &lt;string&gt; — your transcripts.fasta. That's it, that's the non-negotiable. 🙈

🎀 Common options 🎀

the ones you'll actually be reaching for, bestie:

  • --retain_long_orfs_mode &lt;string&gt; — either 'dynamic' or 'strict' (default: dynamic). In dynamic mode, it sets the range according to 1%FDR in random sequence of same GC content. 🧬
  • --retain_long_orfs_length &lt;int&gt; — under 'strict' mode, retain all ORFs found that are equal or longer than these many nucleotides, even if no other evidence marks it as coding (default: 1000000). And yes, that default is so huge it's essentially turned off by default, so it's basically ✨ decorative ✨ until you change it.
  • --retain_pfam_hits &lt;string&gt; — the domain table output file from running hmmscan to search Pfam (see transdecoder.github.io for info). Any ORF with a pfam domain hit will be retained in the final output. 🔍
  • --retain_blastp_hits &lt;string&gt; — blastp output in '-outfmt 6' format. Any ORF with a blast match will be retained in the final output. 🎯
  • --single_best_only — retain only the single best orf per transcript (prioritized by homology then orf length). One winner per transcript, main character energy only. 👑
  • --output_dir, -O &lt;string&gt; — same output directory from the TransDecoder.LongOrfs. Keep the siblings in the same house, fr fr. 🏠
  • --no_refine_starts — start refinement identifies potential start codons for 5' partial ORFs using a PWM, and the process is on by default. So this flag = turning that default off. 🚫

🔥 Advanced options 🔥

for when you're feeling brave and/or your advisor is breathing down your neck:

  • -T &lt;int&gt; — top longest ORFs to train Markov Model (hexamer stats) (default: 500). Note, 10x this value are first selected for removing redundancies, and then this -T value of longest ORFs are selected from the non-redundant set. So like, the funnel is real. 🌀
  • --genetic_code, -G &lt;string&gt; — genetic code (default: universal; see PerlDoc; options: Euplotes, Tetrahymena, Candida, Acetabularia, ...). Full list of Genetic Codes (derived from: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi) coming right up, and yes we're listing all of them because thoroughness is a love language: 🧚
    1. Acetabularia
    2. Candida
    3. Ciliate
    4. Dasycladacean
    5. Euplotid
    6. Hexamita
    7. Mesodinium
    8. Mitochondrial-Ascidian
    9. Mitochondrial-Chlorophycean
    10. Mitochondrial-Echinoderm
    11. Mitochondrial-Flatworm
    12. Mitochondrial-Invertebrates
    13. Mitochondrial-Protozoan
    14. Mitochondrial-Pterobranchia
    15. Mitochondrial-Scenedesmus_obliquus
    16. Mitochondrial-Thraustochytrium
    17. Mitochondrial-Trematode
    18. Mitochondrial-Vertebrates
    19. Mitochondrial-Yeast
    20. Pachysolen_tannophilus
    21. Peritrich
    22. SR1_Gracilibacteria
    23. Tetrahymena
    24. Universal
ok and that's the whole thing, no secrets, no withheld lore. go predict some coding regions bestie, you're gonna ate. 💖

🌺 and that's a wrap from TransDecoder.Predict 6.0.0, dated May 2026 — catch you in the next manpage, mwah 🫶✨

📦 where this page comes from