SHOWSEQ(1e)

📦 version 6.6.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 SHOWSEQ(1e) 💖

okay bestie, welcome to the SHOWSEQ(1e) page straight outta the EMBOSS Manual for Debian ✨ it's literally the glow-up your sequences deserve.

🌸 NAME 🌸

showseq — Displays sequences with features in pretty format 💅

📜 SYNOPSIS

showseq -sequence seqall -mfile datafile -format list -things list
        [-translate range] [-revtranslate range] [-uppercase range]
        [-highlight range] [-annotation range] [-enzymes string]
        [-table list] [-sourcematch string] [-typematch string]
        [-sensematch integer] [-minscore float] [-maxscore float]
        [-tagmatch string] [-valuematch string] [-stricttags boolean]
        -flatreformat boolean -mincuts integer -maxcuts integer
        -sitelen integer -single boolean -blunt boolean -sticky boolean
        -ambiguity boolean -plasmid boolean -methylation boolean
        -commercial boolean -limit boolean -orfminsize integer
        -threeletter boolean -number boolean -width integer
        -length integer -margin integer -name boolean
        -description boolean -offset integer -html boolean
        -outfile outfile

showseq -help

🦋 DESCRIPTION 🦋

so showseq is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). no cap, that's the actual name, it's a whole acronym situation 😌

it belongs to the "Nucleic:Translation,Nucleic:Restriction" command group(s). yes queen, two groups, she's versatile 💅

✨ OPTIONS ✨

🌷 Input section

  • -sequence seqall — that's it, that's the option. the original page gives her no description, she's mysterious like that 🙈
  • -mfile datafile — Default value: Emethylsites.dat

🎀 Required section

  • -format list — Default value: 2
  • -things list — Specify a list of one or more code characters in the order in which you wish things to be displayed one above the other down the page. For example if you wish to see things displayed in the order: sequence, complement sequence, ticks line, frame 1 translation, blank line; then you should enter 'S,C,T,1,B'. Default value: B,N,T,S,A,F

🌈 Additional section

  • -translate range — Regions to translate (if translating). If this is left blank the complete sequence is translated. 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
  • -revtranslate range — Regions to translate (if translating). If this is left blank the complete sequence is translated. 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: 78-56, 45-24, 888..765, 99=67; 45:1
  • -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'.
  • -annotation range — Regions to annotate by marking. If this is left blank, then no annotation is added. A set of regions is specified by a set of pairs of positions followed by optional text. The positions are integers. They are followed by any text (but not digits when on the command-line). Examples of region specifications are: 24-45 new domain 56-78 match to Mouse 1-100 First part 120-156 oligo. A file of ranges to annotate (one range per line) can be specified as '@filename'.
  • -enzymes string — 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. You can 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

  • -table list — no description given on the original page. she simply exists 🫶

🔥 Feature display options

  • -sourcematch string — By default any feature source in the feature table is shown. You can set this to match any feature source you wish to show. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from. The source may be wildcarded by using '*'. If you wish to show more than one source, separate their names with the character '|', eg: gene* | embl. Default value: *
  • -typematch string — By default any feature type in the feature table is shown. You can set this to match any feature type you wish to show. See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature types. The type may be wildcarded by using '*'. If you wish to show more than one type, separate their names with the character '|', eg: *UTR | intron. Default value: *
  • -sensematch integer — By default any feature type in the feature table is shown. You can set this to match any feature sense you wish to show. 0 - any sense, 1 - forward sense, -1 - reverse sense
  • -minscore float — Minimum score of feature to display (see also maxscore). Default value: 0.0
  • -maxscore float — Maximum score of feature to display. If both minscore and maxscore are zero (the default), then any score is ignored. Default value: 0.0
  • -tagmatch string — Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Some of these tags also have values, for example '/gene' can have the value of the gene name. By default any feature tag in the feature table is shown. You can set this to match any feature tag you wish to show. The tag may be wildcarded by using '*'. If you wish to show more than one tag, separate their names with the character '|', eg: gene | label. Default value: *
  • -valuematch string — Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Only some of these tags can have values, for example '/gene' can have the value of the gene name. By default any feature tag value in the feature table is shown. You can set this to match any feature tag value you wish to show. The tag value may be wildcarded by using '*'. If you wish to show more than one tag value, separate their names with the character '|', eg: pax* | 10. Default value: *
  • -stricttags boolean — By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed. If this is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed. Default value: N

👑 Advanced section

🧚 Restriction map options

  • -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
  • -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
  • -sitelen integer — This sets the minimum length of the restriction enzyme recognition site. Any enzymes with sites shorter than this will be ignored. Default value: 4
  • -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. 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. Default value: N
  • -methylation boolean — If this is set then RE recognition sites will not match methylated bases. Default value: N
  • -commercial boolean — turn this on and we only go looking for enzymes that actually have a commercial supplier, bestie. 💸 Important plot twist tho: this qualifier gets ignored if you handed over an explicit list of enzymes to search for instead of just asking for 'all' of them from the REBASE database. The logic is kinda iconic actually — if you're naming a specific enzyme, you probably already know where to get it, so every enzyme name you asked for that cuts will get reported, commercial supplier or not. Default value: Y
  • -limit boolean — this one keeps things chill and only reports one enzyme from each group of isoschizomers. 🫶 The chosen one (the main character of the isoschizomer group, fr) is the prototype listed in the data file 'embossre.equ', which gets created by the program 'rebaseextract'. Want different prototypes? Make a copy of embossre.equ in your home directory and edit it, no cap. If this is set to false then all of the input enzymes will be reported. Lowkey you might wanna set it to false if you're supplying an explicit set of enzymes instead of searching 'all' of them. Default value: Y
  • -orfminsize integer — sets the minimum size of Open Reading Frames (ORFs) to display in the translations. ✨ Every other translation region gets masked by changing the amino acids into '-' characters. Masked. Gone. Not invited. 💅
  • -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 false if you don't wanna display the ID name of the sequence. 🙈 Default value: Y
  • -description boolean — set this to false if you don't wanna display the description of the sequence. 🙈 Default value: Y
  • -offset integer — Default value: 1
  • -html boolean — Default value: N

🌈 Output section 🌈

  • -outfile outfile

💀 BUGS 💀

Found a bug? Not the vibe, but okay, it happens. Report it to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or go straight to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). 🐛

👀 SEE ALSO 👀

showseq 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. (The script did the work, they get the credit, that's the arrangement. 🎀)

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.

And that's the whole page, bestie!! 🦋 You just read a manual page from EMBOSS 6.4.0, dated 05/11/2012, and honestly? You ate. Go sequence something iconic. 💖✨

📦 where this page comes from