TRANSDECODER.LONGORFS(1)

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version 6.0.0 · 2 versions
, in ubuntu stonking

💅 TRANSDECODER.LONGORFS(1)

hiii bestie 🫶 welcome to section 1 of the manual — User Commands — and this one's all about TransDecoder.LongOrfs. she's the opening act of the TransDecoder pipeline and honestly she's serving Transcriptome Protein Prediction. no cap, she extracts long ORFs and that is literally her entire personality. 💖

🌸 NAME 🌸

TransDecoder.LongOrfs — extract long ORFs ✨

🧬 DESCRIPTION 🧬

ok so the original page opens with this ASCII banner and I am not touching it, because it's iconic and also it is the whole vibe. here she is, unedited, exactly as she came into this world:

########################################################################################
#             ______                 ___                  __ #
/_  __/______ ____ ___ / _ \___ _______  ___/ /__ ____ #             / /
/ __/ _ `/ _\(_-</ // / -_) __/ _ \/ _  / -_) __/ #            /_/ /_/
\_,_/_//_/___/____/\__/\__/\___/\_,_/\__/_/   .LongOrfs #
########################################################################################
# #  Transdecoder.LongOrfs|http://transdecoder.github.io> -
Transcriptome Protein Prediction # # #  Required: # #    -t <string>
transcripts.fasta # #  Optional: # #   --gene_trans_map <string>
gene-to-transcript identifier mapping file (tab-delimited,
gene_id<tab>trans_id<return> ) # #   -m <int>
minimum protein length (default: 100) # #   -S
strand-specific (only analyzes top strand) # #   --output_dir | -O
<string>            path to intended output directory # #
--genetic_code | -G <string>                            genetic code
(default: universal; see PerlDoc; options: Euplotes, Tetramena,
Candida, Acetabularia) #
Genetic Codes (derived from:
https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)# Acetabularia
Candida Ciliate Dasycladacean Euplotid Hexamita Mesodinium
Mitochondrial-Ascidian Mitochondrial-Chlorophycean
Mitochondrial-Echinoderm Mitochondrial-Flatworm
Mitochondrial-Invertebrates Mitochondrial-Protozoan
Mitochondrial-Pterobranchia Mitochondrial-Scenedesmus_obliquus
Mitochondrial-Thraustochytrium Mitochondrial-Trematode
Mitochondrial-Vertebrates Mitochondrial-Yeast Pachysolen_tannophilus
Peritrich SR1_Gracilibacteria Tetramena Universal # #
--complete_orfs_only                   yields only complete ORFs (peps
start with Met (M), end with stop (*)) #
#########################################################################################

and for anyone whose eyes just glazed over at the block art 🌈 — the tl;dr is that Transdecoder.LongOrfs lives at http://transdecoder.github.io and its job title is Transcriptome Protein Prediction. that's the moment. that's the whole thing.

now let's get into what she actually wants from you, because she has opinions and she's not shy about them 💅

🎀 Required

  • -t <string> — the transcripts. she wants transcripts.fasta, and she wants it every single time. this is not optional, bestie, this is mandatory. no transcripts, no ORFs, no protein prediction, no nothing. 😭

👑 Optional

  • --gene_trans_map <string> — a gene-to-transcript identifier mapping file. and she's specific about it: it's tab-delimited, formatted as gene_id<tab>trans_id<return>. so that's the gene id, a tab, the transcript id, and a return. in that order. she will notice if you switch them up. 🙈
  • -m <int> — minimum protein length. default is 100. crank it up if you only want the long queens. 📏
  • -S — strand-specific mode. when this is on, she only analyzes the top strand. one strand. top only. that's the rule. iykyk 🦋
  • --output_dir | -O <string> — path to intended output directory. this is where the good stuff gets dropped, so point her somewhere you'll actually find it. 🌸
  • --genetic_code | -G <string> — the genetic code. default is universal, see PerlDoc for the full lore, and the options she's calling out here are Euplotes, Tetramena, Candida, Acetabularia. 🧬

✨ Genetic Codes (derived from: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi) ✨

here's the full roster, not a single one cut, because we don't do half-finished around here 👑

  • Acetabularia
  • Candida
  • Ciliate
  • Dasycladacean
  • Euplotid
  • Hexamita
  • Mesodinium
  • Mitochondrial-Ascidian
  • Mitochondrial-Chlorophycean
  • Mitochondrial-Echinoderm
  • Mitochondrial-Flatworm
  • Mitochondrial-Invertebrates
  • Mitochondrial-Protozoan
  • Mitochondrial-Pterobranchia
  • Mitochondrial-Scenedesmus_obliquus
  • Mitochondrial-Thraustochytrium
  • Mitochondrial-Trematode
  • Mitochondrial-Vertebrates
  • Mitochondrial-Yeast
  • Pachysolen_tannophilus
  • Peritrich
  • SR1_Gracilibacteria
  • Tetramena
  • Universal

🔥 and one more, still in the optional pile

  • --complete_orfs_only — yields only complete ORFs. and "complete" means the peps start with Met (M) and end with stop (*). start with an M, finish with a star, no loose ends, no cliffhangers. clean edges only, periodt ✨
heads up bestie 🫶 — -m defaults to 100, the genetic code defaults to universal, and -S changes what she even looks at (top strand only). don't be surprised when the output changes, you asked for that. 💀

and that's her!! TransDecoder.LongOrfs, version 6.0.0, dated May 2026, page TRANSDECODER.LONGORFS(1) — go extract some long ORFs, you absolute main character 🎀👑💜

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