REMAP(1e)

💖 REMAP(1e) 💖

okay bestie, sit down, hydrate, because we're about to read a whole manual page together and honestly? it's giving iconic. this one lives in the EMBOSS Manual for Debian, and the program itself is called remap. it's a command line situation, it's from EMBOSS (aka "the European Molecular Biology Open Software Suite" — yes that's the real name, they ate), and it hangs out in the "Display,Nucleic:Restriction,Nucleic:Translation" command group(s). so like, restriction + translation + display, a whole vibe. 🧬✨

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🌸 NAME 🌸

remap — Display restriction enzyme binding sites in a nucleotide sequence 💅

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🎀 SYNOPSIS 🎀

remap -sequence seqall -mfile datafile -enzymes string -sitelen integer
      [-mincuts integer] [-maxcuts integer] [-single boolean]
      [-blunt boolean] [-sticky boolean] [-ambiguity boolean]
      [-plasmid boolean] [-methylation boolean] [-commercial boolean]
      [-table list] [-frame list] -outfile outfile [-cutlist boolean]
      [-flatreformat boolean] [-limit boolean] -translation boolean
      -reverse boolean -orfminsize integer -uppercase range
      -highlight range -threeletter boolean -number boolean
      -width integer -length integer -margin integer -name boolean
      -description boolean -offset integer -html boolean

remap -help

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🦋 DESCRIPTION 🦋

so remap is a command line program from EMBOSS (the European Molecular Biology Open Software Suite, we said it, we love it). it's part of the "Display,Nucleic:Restriction,Nucleic:Translation" command group(s), which, no cap, is exactly the energy you'd expect from a tool that finds where enzymes cut your sequence. 🔥

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✨ OPTIONS ✨

💜 Input section 💜

• -sequence seqall — your sequence goes here, bestie.
• -mfile datafile — Default value: Emethylsites.dat

🌈 Required section 🌈

• -enzymes string — which enzymes are we hunting for? The name 'all' reads in all enzyme names from the REBASE database. You can specify enzymes by giving their names with commas between then, such as: 'HincII,hinfI,ppiI,hindiii'. The case of the names is not important (slay, lowercase enjoyers stay winning). You can also specify a file of enzyme names to read in by giving the name of the file holding the enzyme names with a '@' character in front of it, for example, '@enz.list'. Blank lines and lines starting with a hash character or '!' are ignored, and all other lines are 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

• -sitelen integer — this sets the minimum length of the restriction enzyme recognition site. Any enzymes with sites shorter than this will be ignored. like, not even invited to the group chat. Default value: 4

🌟 Additional section 🌟

• -mincuts integer — this sets the minimum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut fewer times than this will be ignored. Default value: 1
• -maxcuts integer — this sets the maximum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut more times than this will be ignored. Default value: 2000000000 (yes really, that's the number, she's generous 💀)
• -single boolean — if this is set then this 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. (so dramatic, but okay.) Default value: N
• -blunt boolean — this allows those enzymes which cut at the same position on the forward and reverse strands to be considered. Default value: Y
• -sticky boolean — this allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered. Default value: Y
• -ambiguity boolean — this allows those enzymes which have one or more 'N' ambiguity codes in their pattern to be considered. Default value: Y
• -plasmid boolean — if this is set then this allows searches for restriction enzyme recognition site and cut positions that span the end of the sequence to be considered. (circular brain moment 🌀) Default value: N
• -methylation boolean — if this is set then RE recognition sites will not match methylated bases. Default value: N
• -commercial boolean — if this is set, then only those enzymes with a commercial supplier will be searched for. Heads up: this qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through 'all' the enzymes in the REBASE database. The logic being: it is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from, and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier. periodt. Default value: Y
• -table list
• -frame list — this allows you to specify the frames that are translated. If you are not displaying cut sites on the reverse sense, then the reverse sense translations will not be displayed even if you have requested frames 4, 5 or 6. By default, all six frames will be displayed. Default value: 6

👑 Output section 👑

• -outfile outfile — where the good stuff goes.
• -cutlist boolean — this produces lists in the output of the enzymes that cut, those that cut but are excluded because that cut fewer times than mincut or more times than maxcut, and those enzymes that do not cut. (a full breakdown, we love receipts 🧾) Default value: Y
• -flatreformat boolean — this changes the output format to one where the recognition site is indicated by a row of '===' characters and the cut site is pointed to by a '>' character in the forward sense, or a '<' in the reverse sense strand. Default value: N
• -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 are supplying an explicit set of enzymes rather than searching 'all' of them. Default value: Y
• -translation boolean — this displays the 6-frame translations of the sequence in the output. Default value: Y
• -reverse boolean — this displays the cut sites and translation of the reverse sense. Default value: Y
• -orfminsize integer — this sets the minimum size of Open Reading Frames (ORFs) to display in the translations. All other translation regions are masked by changing the amino acids to '-' characters.
• -uppercase range — Regions to put in uppercase. If this is left blank, then the sequence case is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-digit, non-alpha character. Examples of region specifications are:

24-45, 56-78
1:45, 67=99;765..888
1,5,8,10,23,45,57,99

• -highlight range — Regions to colour if formatting for HTML. If this is left blank, then the sequence is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are followed by any valid HTML font colour. Examples of region specifications are:

24-45 blue
56-78 orange
1-100 green
120-156 red

A file of ranges to colour (one range per line) can be specified as '@filename'.

• -threeletter boolean — Default value: N
• -number boolean — Default value: N
• -width integer — Default value: 60
• -length integer
• -margin integer — Default value: 10
• -name boolean — Set this to be false if you do not wish to display the ID name of the sequence. Default value: Y
• -description boolean — Set this to be false if you do not wish to display the description of the sequence. Default value: Y
• -offset integer — Default value: 1
• -html boolean — Default value: N

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💀 BUGS 💀

found a bug? (not me manifesting it, just covering bases.) 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 🫶

remap is fully documented via the tfm(1) system. 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 autogen girlies carried 🙈)

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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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and that's the whole page, bestie, no notes. 🌈 this little masterpiece is EMBOSS 6.4.0, dated 05/11/2012, and it's the REMAP(1e) page in the EMBOSS Manual for Debian. go cut some sequences, you absolute icon. 🎀🦋✨💅