GT-LTRDIGEST(1)

💖 GT-LTRDIGEST(1) 💖

okay so bestie, you're in the GenomeTools Manual and this is gt-ltrdigest — the lil icon that goes and finds + annotates sequence features inside LTR retrotransposon candidates. yes, retrotransposons. we're doing jumping genes today, slay. 🧬✨

---

✨ NAME ✨

gt-ltrdigest — Identifies and annotates sequence features in LTR retrotransposon candidates.

🫶 SYNOPSIS 🫶

gt ltrdigest [option ...] gff3_file

🌸 DESCRIPTION 🌸

like, here's the whole entire vibe. every option, no skips, we don't gatekeep in this house. 👑

• -outfileprefix [string] — prefix for output files (e.g. foo will create files called foo_*.csv and foo_*.fas). Omit this option for GFF3 output only.
• -metadata [yes|no] — output metadata (run conditions) to separate file (default: yes)
• -seqnamelen [value] — set maximal length of sequence names in FASTA headers (e.g. for clustalw or similar tools) (default: 20)
• -pptlen [start end] — required PPT length range (default: [8..30])
• -uboxlen [start end] — required U-box length range (default: [3..30])
• -uboxdist [value] — allowed U-box distance range from PPT (default: 0)
• -pptradius [value] — radius around beginning of 3' LTR to search for PPT (default: 30)
• -pptrprob [value] — purine emission probability inside PPT (default: 0.970000)
• -pptyprob [value] — pyrimidine emission probability inside PPT (default: 0.030000)
• -pptgprob [value] — background G emission probability outside PPT (default: 0.250000)
• -pptcprob [value] — background C emission probability outside PPT (default: 0.250000)
• -pptaprob [value] — background A emission probability outside PPT (default: 0.250000)
• -ppttprob [value] — background T emission probability outside PPT (default: 0.250000)
• -pptuprob [value] — U/T emission probability inside U-box (default: 0.910000)
• -trnas [filename] — tRNA library in multiple FASTA format for PBS detection. Omit this option to disable PBS search.
• -pbsalilen [start end] — required PBS/tRNA alignment length range (default: [11..30])
• -pbsoffset [start end] — allowed PBS offset from LTR boundary range (default: [0..5])
• -pbstrnaoffset [start end] — allowed PBS/tRNA 3' end alignment offset range (default: [0..5])
• -pbsmaxedist [value] — maximal allowed PBS/tRNA alignment unit edit distance (default: 1)
• -pbsradius [value] — radius around end of 5' LTR to search for PBS (default: 30)
• -hmms — profile HMM models for domain detection (separate by spaces, finish with --) in HMMER3 format. Omit this option to disable pHMM search.
• -pdomevalcutoff [value] — global E-value cutoff for pHMM search, default 1E-6
• -pdomcutoff [...] — model-specific score cutoff. choose from TC (trusted cutoff) | GA (gathering cutoff) | NONE (no cutoffs) (default: NONE)
• -aliout [yes|no] — output pHMM to amino acid sequence alignments (default: no)
• -aaout [yes|no] — output amino acid sequences for protein domain hits (default: no)
• -allchains [yes|no] — output features from all chains and unchained features, labeled with chain numbers (default: no)
• -maxgaplen [value] — maximal allowed gap size between fragments (in amino acids) when chaining pHMM hits for a protein domain (default: 50)
• -force_recreate [yes|no] — force recreation of hmmpressed profiles (default: no)
• -pbsmatchscore [value] — match score for PBS/tRNA alignments (default: 5)
• -pbsmismatchscore [value] — mismatch score for PBS/tRNA alignments (default: -10)
• -pbsinsertionscore [value] — insertion score for PBS/tRNA alignments (default: -20)
• -pbsdeletionscore [value] — deletion score for PBS/tRNA alignments (default: -20)
• -v [yes|no] — be verbose (default: no)
• -o [filename] — redirect output to specified file (default: undefined)
• -gzip [yes|no] — write gzip compressed output file (default: no)
• -bzip2 [yes|no] — write bzip2 compressed output file (default: no)
• -force [yes|no] — force writing to output file (default: no)
• -seqfile [filename] — set the sequence file from which to take the sequences (default: undefined)
• -encseq [filename] — set the encoded sequence indexname from which to take the sequences (default: undefined)
• -seqfiles — set the sequence files from which to extract the features. use -- to terminate the list of sequence files
• -matchdesc [yes|no] — search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match (default: no)
• -matchdescstart [yes|no] — exactly match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) from the beginning to the first whitespace (default: no)
• -usedesc [yes|no] — use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries. If a description contains a sequence range (e.g., III:1000001..2000000), the first part is used as sequence ID (III) and the first range position as offset (1000001) (default: no)
• -regionmapping [string] — set file containing sequence-region to sequence file mapping (default: undefined)
• -help — display help for basic options and exit
• -help+ — display help for all options and exit
• -version — display version information and exit

---

😭 REPORTING BUGS 😭

found something cursed? Report bugs to https://github.com/genometools/genometools/issues.

---

and that's the whole thing bestie!! 🎀 this page is from GenomeTools 1.6.6, dated 11/09/2025 — so if you're reading this in the future, no cap, check if there's a newer one. bye pookie, go annotate some transposons 💅✨