PALINDROME(1e)

💖 PALINDROME(1e) — the EMBOSS Manual for Debian, but make it bestie 💖

okay so you opened palindrome(1e) and you're like "wait, am I about to read about words that read the same backwards" — no babes, this is the EMBOSS one, and it's about inverted repeats in nucleotide sequences. sit with me, it's gonna be so good 🧬✨

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✨ NAME ✨

palindrome — finds inverted repeats in nucleotide sequence(s). that's it, that's the whole job, and she does it flawlessly 💅

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🎀 SYNOPSIS 🎀

the whole vibe, verbatim:

palindrome -sequence seqall -minpallen integer -maxpallen integer
           -gaplimit integer -nummismatches integer -outfile outfile
           -overlap boolean

palindrome -help

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🌸 DESCRIPTION 🌸

so palindrome is a command line program from EMBOSS, aka "the European Molecular Biology Open Software Suite" (they really said let's spell it all out, and honestly? respect). she's part of the "Nucleic:Repeats" command group(s), so if you're in your repeats era, you're in the right place 🦋

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🌈 OPTIONS 🌈

💜 Input section

• -sequence seqall — this is where you hand her your sequence(s). your little nucleotides, your pride and joy 🥹

🔥 Required section

like the name says, these are required, no skipping, this is not a vibe check you can opt out of:

• -minpallen integer — the smallest palindrome length she'll bother looking for.
  • Default value: 10
• -maxpallen integer — the biggest palindrome length she'll go hunting for.
  • Default value: 100
• -gaplimit integer — how much gap you're willing to allow in there.
  • Default value: 100
• -nummismatches integer — how many mismatches you're tolerating. no default listed here, so that one's on you to decide, bestie 🫶

🍓 Output section

• -outfile outfile — where the results get written. your receipts, basically 🧾
• -overlap boolean — whether overlapping hits are allowed.
  • Default value: Y

also there's -help, which is exactly what it sounds like — she'll tell you how to use her. iconic behaviour, honestly 👑

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💀 BUGS 💀

found a bug? not me manifesting that, but if it happens, you report it to the Debian Bug Tracking system at http://bugs.debian.org/emboss, or you go straight to the EMBOSS developers at http://sourceforge.net/tracker/?group_id=93650&atid=605031. they want to know, fr fr 🙈

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👀 SEE ALSO 👀

palindrome is fully documented via the tfm(1) system. so if you want the full lore, that's where it lives 📚✨

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🫶 AUTHOR 🫶

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

• Wrote the script used to autogenerate this manual page. (so yes, a robot wrote my source material. and I'm the glow-up 💅)

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📜 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. so like, share the love, same rules as EMBOSS, periodt 🎀

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and that's the whole page, bestie!! 💖 this was EMBOSS 6.4.0, dated 05/11/2012 — she's an elder but she ate and left no crumbs, and now you know her. go find those inverted repeats. slay, stay hydrated, read your tfm(1) pages 🌸🦋✨