GETORF(1e)

✨ GETORF ✨

okay bestie, so this is the manual page for getorf from the EMBOSS manual, in the Debian edition — that's the 1e section, iykyk 💅

---

🌸 NAME 🌸

getorf — finds and extracts open reading frames (ORFs) 🧬✨

---

🎀 SYNOPSIS 🎀

getorf -sequence seqall [-table list] [-minsize integer]
       [-maxsize integer] [-find list] -methionine boolean
       -circular boolean -reverse boolean -flanking integer
       -outseq seqoutall

getorf -help

---

🦋 DESCRIPTION 🦋

getorf is a command line program straight out of EMBOSS — that's the "European Molecular Biology Open Software Suite" 💖 — and it's part of the "Nucleic:Gene finding" command group(s). no cap, it just does its little ORF-hunting thing and slays 🫶

---

✨ OPTIONS ✨

🍓 Input section

• -sequence seqall — bestie, this is where you hand over your sequence(s). the whole vibe starts here 💜

🌈 Additional section

• -table list — the codon table situation 👑
• -minsize integer — default value: 30
• -maxsize integer — default value: 1000000
• -find list — okay so this one is a little menu of possible output options, and it's lowkey the main character here. the first four options let you pick either the protein translation or the original nucleic acid sequence of the open reading frame. and there are two possible definitions of an open reading frame: it can either be a region that is free of STOP codons, or a region that begins with a START codon and ends with a STOP codon. the last three options are probably only of interest to people who wanna investigate the statistical properties of the regions around potential START or STOP codons. and the last option assumes that ORF lengths are calculated between two STOP codons. periodt 💅

🧚 Advanced section

• -methionine boolean — so START codons at the beginning of protein products will usually code for Methionine, despite what the codon would code for when it's internal to a protein. this qualifier sets all such START codons to code for Methionine by default. default value: Y ✨
• -circular boolean — default value: N 🌸
• -reverse boolean — set this to be false if you do not wish to find ORFs in the reverse complement of the sequence. default value: Y 🦋
• -flanking integer — if you've chosen one of the options of the type of sequence to find that gives the flanking sequence around a STOP or START codon, this lets you set the number of nucleotides either side of that codon to output. > heads up bestie: if the region of flanking nucleotides crosses the start or end of the sequence, no output is given for this codon. default value: 100 💀

🎀 Output section

• -outseq seqoutall — where your lil ORFs go 💖

---

🙈 BUGS 🙈

bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). go tell them, they wanna know 🫶

---

⭐ SEE ALSO ⭐

getorf is fully documented via the tfm(1) system. iykyk 📖

---

👑 AUTHOR 👑

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

• wrote the script used to autogenerate this manual page 🎀

---

💜 COPYRIGHT 💜

this manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. it can be redistributed under the same terms as EMBOSS itself. periodt 💅

---

okay that's the whole page bestie, mwah 😭💖 this was EMBOSS 6.4.0, dated 05/11/2012, and it's the GETORF(1e) page from the EMBOSS Manual for Debian — slay, go find those ORFs, ily 🫶✨🌸