RESTRICT(1e)

💖 RESTRICT — like, the whole vibe 💖

Okay bestie, listen. This is the restrict page from the EMBOSS Manual for Debian — RESTRICT(1e), one of those fancy section-1e joint manuals. It's giving "I read my DNA for fun" energy and honestly? Iconic.

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🌸 NAME 🌸

restrict — reports restriction enzyme cleavage sites in a nucleotide sequence. Yes literally that. It's the enzyme detective. 🕵️♀️✨

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✨ SYNOPSIS ✨

restrict -sequence seqall -datafile datafile -mfile datafile
         -sitelen integer -enzymes string -min integer -max integer
         -solofragment boolean -single boolean -blunt boolean
         -sticky boolean -ambiguity boolean -plasmid boolean
         -methylation boolean -commercial boolean -limit boolean
         -alphabetic boolean -fragments boolean -name boolean
         -outfile report

restrict -help

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🦋 DESCRIPTION 🦋

So. restrict is a command line program from EMBOSS — that's "the European Molecular Biology Open Software Suite" 💅 — and it lives in the "Nucleic:Restriction" command group(s). That's its whole little neighborhood. No cap.

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🎀 OPTIONS 🎀

🍓 Input section 🍓

• -sequence seqall — yeah bestie, that's the sequence input. That's it, that's the line.
• -datafile datafile — the data file. Same energy, no extra lore attached.
• -mfile datafile — the methylation sites file, and the default is Emethylsites.dat.

👑 Required section 👑

• -sitelen integer — this sets the minimum length of the restriction enzyme recognition site. Any enzyme whose site is shorter than this gets straight-up ignored, ghosted, blocked. Default value: 4.
• -enzymes string — okay this one is the main character. The name all reads in all the enzyme names from the REBASE database. You can also name enzymes yourself, commas between them, like this: 'HincII,hinfI,ppiI,hindiii'. The case of the names does not matter — type it however your heart desires, she doesn't care. 🫶

You can also point it at a file of enzyme names: stick a @ character in front of the filename, like '@enz.list'. Blank lines get ignored. Lines starting with a hash character or ! get ignored. Everything else gets concatenated together with a comma character ',' and then treated as the list of enzymes to search for. An example of a file of enzyme names is: ! my enzymes HincII, ppiII ! other enzymes hindiii HinfI PpiI

Default value: all.

🌈 Advanced section 🌈

• -min integer — the minimum number of cuts for any restriction enzyme that'll even be considered. Cut fewer times than this and you're out, sorry. Default value: 1.
• -max integer — the maximum number of cuts for any restriction enzyme that'll be considered. Cut more times than this and, yeah, ignored. Default value: 2000000000. (yes that is a real number, she's generous ✨)
• -solofragment boolean — this gives you the fragment lengths of the forward sense strand produced by complete restriction by each restriction enzyme on its own. Results get added to the tail section of the report. Default value: N.
• -single boolean — if you set this, it forces the values of the mincuts and maxcuts qualifiers to both be 1. Any other value you may have set them to will be ignored. Just. Overruled. Default value: N.
• -blunt boolean — allows those enzymes that cut at the same position on the forward and reverse strands to be considered. Default value: Y.
• -sticky boolean — allows those enzymes that cut at different positions on the forward and reverse strands — leaving an overhang, you know the vibe — to be considered. Default value: Y.
• -ambiguity boolean — allows those enzymes that have one or more 'N' ambiguity codes in their pattern to be considered. Default value: Y.
• -plasmid boolean — if you set this, it allows searches for restriction enzyme recognition site and cut positions that span the end of the sequence to be considered. Default value: N.
• -methylation boolean — if you set this, RE recognition sites will not match methylated bases. Default value: N.
• -commercial boolean — if you set this, then only enzymes with a commercial supplier get searched for. But listen, this qualifier is ignored if you've specified an explicit list of enzymes to search for instead of going through 'all' the enzymes in the REBASE database. The reasoning, per the page: it's assumed that if you're asking for an explicit enzyme, then you probably know where to get it from — so all the enzyme names you asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier. She trusts you, bestie. Default value: Y.

💅 Output section 💅

• -limit boolean — this limits the reporting of enzymes to just one enzyme from each group of isoschizomers. The enzyme chosen to represent an isoschizomer group is the prototype indicated in the data file 'embossre.equ', which is created by the program 'rebaseextract'. If you prefer different prototypes to be used, make a copy of embossre.equ in your home directory and edit it. If this value is set to be false then all of the input enzymes will be reported. You might like to set this to false if you're supplying an explicit set of enzymes rather than searching 'all' of them. Default value: Y.
• -alphabetic boolean — Default value: N.
• -fragments boolean — this gives the fragment lengths of the forward sense strand produced by complete restriction using all of the input enzymes together. Results get added to the tail section of the report. Default value: N.
• -name boolean — Default value: N.
• -outfile report — where the report goes. The output file. That's the one. 💖

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💀 BUGS 💀

Found a bug? Not on my watch, but okay. 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).

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👀 SEE ALSO 👀

restrict is fully documented via the tfm(1) system. Go read that too, iykyk.

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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. (the script is the real author, we're all just living in its house 🏠)

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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.

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Heads up bestie: this whole thing was autogenerated, so if something reads weird, blame the Ajax Control Definition, not me 💀

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And that's the page, fr fr. It came from EMBOSS 6.4.0, dated 05/11/2012, and it's the RESTRICT(1e) manual — section 1e, manual page restrict. Slay, go restrict something. 🧬💜🎀