| showseq

## Function

Display a sequence with features, translation etc

## Description

showseq displays a protein or a nucleic acid sequence in a style suitable for publication.

The output is sent to the screen by default for the user to view, but it can write the results to a file.

The display style of the output is very flexible. The user can select a style from the pre-set choice of formats, or can design a style to suit their purposes and aesthetic tastes.

If designing a new format, you can choose the order in which things are printed around the sequence. The things that you can display are:

    s	Sequence
    b	Blank line
    1	Frame 1 translation
    2	Frame 2 translation
    3	Frame 3 translation
    -1	Frame -1 translation
    -2	Frame -2 translation
    -2	Frame -3 translation
    t	Ticks line
    n	Number ticks line
    c	Complement sequence
    f	Features (from the feature table or from a command line -ufo file)
    r	Restriction enzyme cut sites in the forward sense
    -r	Restriction enzyme cut sites in the reverse sense
    a	User Annotation

The letters for these things can be in upper or lower case.
They can be displayed in any order.

You do not have to make your own format; there is a selection of pre-defined standard formats for you to choose from.

The default standard format displays the following: for every new line that the sequence starts to write, the output display will contain first a blank line ('b'), then the position numbers of the ticks ('n') then the ticks every 10 characters ('t') then the sequence itself ('s') then any user-supplied annotation ('a') then the features from the feature table ('f'). Subsequent lines of the sequence output will repeat this format.

The 'thing' codes used in the list of standard formats are:

    Sequence only:                  S A
    Default sequence:               B N T S A F
    Pretty sequence:                B N T S A
    One frame translation:          B N T S B 1 A F
    Three frame translations:       B N T S B 1 2 3 A F
    Six frame translations:         B N T S B 1 2 3 T -3 -2 -1 A F
    Restriction enzyme map:         B R S N T C -R B 1 2 3 T -3 -2 -1 A
    Baroque:                        B 1 2 3 N T R S T C -R T -3 -2 -1 A F

The displayed sequence can be numbered either by numbering the start and ending positions, or by placing a ruler with ticks above or below the sequence.

The width of a line can be set. The width of a margin around the sequence reserved for numbering can be set. The initial position to start numbering from can be set.

The sequence can be translated, using the selectable genetic code tables. The translation can be done in one, three or six frames. The translation can be displayed in one-letter or three-letter amino acid codes. The translation can optionally be displayed only when it is in open reading frames (ORFs) of a specified minimum size. One or more specified regions of the sequence can be individually translated.

Specified regions of the sequence can be displayed in uppercase to highlight them.

The output can be formatted for HTML.

If the output is being formatted for HTML, then specified regions of the sequence can be displayed in any valid HTML colours.

The Restriction Enzyme database (REBASE) is a collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Most recently, putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed.

The home page of REBASE is: http://rebase.neb.com/

This program can use REBASE data to find the recognition sites and/or cut sites of restriction enzymes in a nucleic acid sequence.

This program can display the cut sites on both strands.

One potentially very useful option is '-flatreformat' that displays not only the cut sites which many other restriction cut-site programs will show, but also shows the recognition site.

If the sequence is in EMBL, Genbank or SwissProt format, the feature table of the sequence can be dispalyed with the sequence. GFF file features can also be displayed if they are included on the command line with the -ufo=file qualifier.

## Usage

Here is a sample session with showseq

    % showseq tembl:x13776 -sbeg 1 -send 100
    Display a sequence with features, translation etc..
    Things to display
             0 : Enter your own list of things to display
             1 : Sequence only
             2 : Default sequence with features
             3 : Pretty sequence
             4 : One frame translation
             5 : Three frame translations
             6 : Six frame translations
             7 : Restriction enzyme map
             8 : Baroque
    Display format [2]:
    Output file [x13776.showseq]:

Go to the input files for this example
Go to the output files for this example

Example 2

The standard list of output formats are only a small selection of the possible ways in which a sequence might be displayed. Precise control over the output format is acheived by selecting the qualifier '-format 0' (Option 0 in the list of things to display). For example, by choosing format '0' and then specifying that we want to display the things: 'b,s,t,c', we will output the sequence in the following way:

    % showseq tembl:x13776 -sbeg 1 -send 120
    Display a sequence with features, translation etc..
    Things to display
             0 : Enter your own list of things to display
             1 : Sequence only
             2 : Default sequence with features
             3 : Pretty sequence
             4 : One frame translation
             5 : Three frame translations
             6 : Six frame translations
             7 : Restriction enzyme map
             8 : Baroque
    Display format [2]: 0
    Specify your own things to display
             S : Sequence
             B : Blank line
             1 : Frame1 translation
             2 : Frame2 translation
             3 : Frame3 translation
            -1 : CompFrame1 translation
            -2 : CompFrame2 translation
            -3 : CompFrame3 translation
             T : Ticks line
             N : Number ticks line
             C : Complement sequence
             F : Features
             R : Restriction enzyme cut sites in forward sense
            -R : Restriction enzyme cut sites in reverse sense
             A : Annotation
    Enter a list of things to display [B,N,T,S,A,F]: b,s,t,c
    Output file [x13776.showseq]:

Go to the output files for this example

Example 3

Display only the sequence:

    % showseq tembl:x13776 -sbeg 1 -send 100 -noname -nodesc -format 0 -thing S
    Display a sequence with features, translation etc..
    Output file [x13776.showseq]:

Go to the output files for this example

Example 4

Protein sequence can be displayed in three-letter codes. (The codes are displayed downwards, so the first code is 'Met'):

    % showseq tsw:rs24_fugru -three -format 2
    Display a sequence with features, translation etc..
    Output file [rs24_fugru.showseq]:

Go to the input files for this example
Go to the output files for this example

Example 5

Number the sequence lines in the margin:

    % showseq tembl:x13776 -sbeg 1 -send 100 -format 1 -number
    Display a sequence with features, translation etc..
    Output file [x13776.showseq]:

Go to the output files for this example

Example 6

Start the numbering at a specified value ('123' in this case):

    % showseq tembl:x13776 -sbeg 1 -send 100 -format 1 -number -offset 123
    Display a sequence with features, translation etc..
    Output file [x13776.showseq]:

Go to the output files for this example

Example 7

Make selected regions uppercase. (Use '-slower' to force the rest of the sequence to be lowercase).

    % showseq tembl:x13776 -sbeg 1 -send 100 -format 1 -slower -upper '25-45,101-203,333-362'
    Display a sequence with features, translation etc..
    Output file [x13776.showseq]:

Go to the output files for this example

Example 8

Translate selected regions:

    % showseq tembl:x13776 -sbeg 1 -send 120 -format 4 -trans 25-49,66-76
    Display a sequence with features, translation etc..
    Output file [x13776.showseq]:

Go to the output files for this example

Example 9

Add your own annotation to the display:

    % showseq tembl:x13776 -sbeg 1 -send 100 -format 2 -send 120 -annotation '13-26 binding site 15-15 SNP'
    Display a sequence with features, translation etc..
    Output file [x13776.showseq]:

Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers (* if not always prompted):
      [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                      format, or reference (input USA)
       -format             menu       [2] Display format (Values: 0 (Enter your
                                      own list of things to display); 1 (Sequence
                                      only); 2 (Default sequence with features); 3
                                      (Pretty sequence); 4 (One frame
                                      translation); 5 (Three frame translations);
                                      6 (Six frame translations); 7 (Restriction
                                      enzyme map); 8 (Baroque))
    *  -things             menu       [B,N,T,S,A,F] 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'. (Values: S
                                      (Sequence); B (Blank line); 1 (Frame1
                                      translation); 2 (Frame2 translation); 3
                                      (Frame3 translation); -1 (CompFrame1
                                      translation); -2 (CompFrame2 translation);
                                      -3 (CompFrame3 translation); T (Ticks line);
                                      N (Number ticks line); C (Complement
                                      sequence); F (Features); R (Restriction
                                      enzyme cut sites in forward sense); -R
                                      (Restriction enzyme cut sites in reverse
                                      sense); A (Annotation))
      [-outfile]           outfile    [*.showseq] Output file name

       Additional (Optional) qualifiers:
       -translate          range      [If this is left blank the complete sequence
                                      is translated.] 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
                                      1,5,8,10,23,45,57,99
       -uppercase          range      [If this is left blank, then the sequence
                                      case is left alone.] 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      [(full sequence)] 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      [If this is left blank, then no annotation
                                      is added.] 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     [all] 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 (Any string is accepted)
       -table              menu       [0] Genetic code to use (Values: 0
                                      (Standard); 1 (Standard (with alternative
                                      initiation codons)); 2 (Vertebrate
                                      Mitochondrial); 3 (Yeast Mitochondrial); 4
                                      (Mold, Protozoan, Coelenterate Mitochondrial
                                      and Mycoplasma/Spiroplasma); 5
                                      (Invertebrate Mitochondrial); 6 (Ciliate
                                      Macronuclear and Dasycladacean); 9
                                      (Echinoderm Mitochondrial); 10 (Euplotid
                                      Nuclear); 11 (Bacterial); 12 (Alternative
                                      Yeast Nuclear); 13 (Ascidian Mitochondrial);
                                      14 (Flatworm Mitochondrial); 15
                                      (Blepharisma Macronuclear); 16
                                      (Chlorophycean Mitochondrial); 21 (Trematode
                                      Mitochondrial); 22 (Scenedesmus obliquus);
                                      23 (Thraustochytrium Mitochondrial))
       -matchsource        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 (Any string is accepted)
       -matchtype          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://www3.ebi.ac.uk/Services/WebFeat/
                                      for a list of the EMBL feature types and see
                                      Appendix A of the Swissprot user manual in
                                      http://www.expasy.ch/txt/userman.txt 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 (Any string is accepted)
       -matchsense         integer    [0 - any sense, 1 - forward sense, -1 -
                                      reverse sense] 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 (Any integer value)
       -minscore           float      [0.0] If this is greater than or equal to
                                      the maximum score, then any score is
                                      permitted (Any numeric value)
       -maxscore           float      [0.0] If this is less than or equal to the
                                      maximum score, then any score is permitted
                                      (Any numeric value)
       -matchtag           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 (Any string is accepted)
       -matchvalue         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 valueyou 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 (Any string is accepted)
       -stricttags         boolean    [N] 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.

       Advanced (Unprompted) qualifiers:
       -flatreformat       boolean    [N] 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.
       -mincuts            integer    [1] 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. (Integer from 1
                                      to 1000)
       -maxcuts            integer    [2000000000] 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. (Integer up
                                      to 2000000000)
       -sitelen            integer    [4] This sets the minimum length of the
                                      restriction enzyme recognition site. Any
                                      enzymes with sites shorter than this will be
                                      ignored. (Integer from 2 to 20)
       -single             boolean    [N] 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.
       -[no]blunt          boolean    [Y] This allows those enzymes which cut at
                                      the same position on the forward and reverse
                                      strands to be considered.
       -[no]sticky         boolean    [Y] This allows those enzymes which cut at
                                      different positions on the forward and
                                      reverse strands, leaving an overhang, to be
                                      considered.
       -[no]ambiguity      boolean    [Y] This allows those enzymes which have one
                                      or more 'N' ambiguity codes in their
                                      pattern to be considered
       -plasmid            boolean    [N] If this is set then this allows searches
                                      for restriction enzyme recognition site and
                                      cut postions that span the end of the
                                      sequence to be considered.
       -[no]commercial     boolean    [Y] If this is set, then only those enzymes
                                      with a commercial supplier will be searched
                                      for. 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. 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.
       -[no]limit          boolean    [Y] 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.
       -orfminsize         integer    [0] 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. (Integer 0 or more)
       -threeletter        boolean    [N] Display protein sequences in
                                      three-letter code
       -number             boolean    [N] Number the sequences
       -width              integer    [60] Width of sequence to display (Integer 1
                                      or more)
       -length             integer    [0] Line length of page (0 for indefinite)
                                      (Integer 0 or more)
       -margin             integer    [10] Margin around sequence for numbering
                                      (Integer 0 or more)
       -[no]name           boolean    [Y] Set this to be false if you do not wish
                                      to display the ID name of the sequence
       -[no]description    boolean    [Y] Set this to be false if you do not wish
                                      to display the description of the sequence
       -offset             integer    [1] Offset to start numbering the sequence
                                      from (Any integer value)
       -html               boolean    [N] Use HTML formatting

       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1            integer    Start of each sequence to be used
       -send1              integer    End of each sequence to be used
       -sreverse1          boolean    Reverse (if DNA)
       -sask1              boolean    Ask for begin/end/reverse
       -snucleotide1       boolean    Sequence is nucleotide
       -sprotein1          boolean    Sequence is protein
       -slower1            boolean    Make lower case
       -supper1            boolean    Make upper case
       -sformat1           string     Input sequence format
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-outfile" associated qualifiers
       -odirectory2        string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write standard output
       -filter             boolean    Read standard input, write standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | (Gapped) sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
-format | Display format |
0 | (Enter your own list of things to display)
1 | (Sequence only)
2 | (Default sequence with features)
3 | (Pretty sequence)
4 | (One frame translation)
5 | (Three frame translations)
6 | (Six frame translations)
7 | (Restriction enzyme map)
8 | (Baroque)
| 2
-things | 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'. |
S | (Sequence)
B | (Blank line)
1 | (Frame1 translation)
2 | (Frame2 translation)
3 | (Frame3 translation)
-1 | (CompFrame1 translation)
-2 | (CompFrame2 translation)
-3 | (CompFrame3 translation)
T | (Ticks line)
N | (Number ticks line)
C | (Complement sequence)
F | (Features)
R | (Restriction enzyme cut sites in forward sense)
-R | (Restriction enzyme cut sites in reverse sense)
A | (Annotation)
| B,N,T,S,A,F
[-outfile] (Parameter 2) | Output file name | Output file | <*>.showseq
Additional (Optional) qualifiers | Allowed values | Default
-translate | 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 1,5,8,10,23,45,57,99 | Sequence range | If this is left blank the complete sequence is translated.
-uppercase | 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 | Sequence range | If this is left blank, then the sequence case is left alone.
-highlight | 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'. | Sequence range | full sequence
-annotation | 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'. | Sequence range | If this is left blank, then no annotation is added.
-enzymes | 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 | Any string is accepted | all
-table | Genetic code to use |
0 | (Standard)
1 | (Standard (with alternative initiation codons))
2 | (Vertebrate Mitochondrial)
3 | (Yeast Mitochondrial)
4 | (Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma)
5 | (Invertebrate Mitochondrial)
6 | (Ciliate Macronuclear and Dasycladacean)
9 | (Echinoderm Mitochondrial)
10 | (Euplotid Nuclear)
11 | (Bacterial)
12 | (Alternative Yeast Nuclear)
13 | (Ascidian Mitochondrial)
14 | (Flatworm Mitochondrial)
15 | (Blepharisma Macronuclear)
16 | (Chlorophycean Mitochondrial)
21 | (Trematode Mitochondrial)
22 | (Scenedesmus obliquus)
23 | (Thraustochytrium Mitochondrial)
| 0
-matchsource | 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 | Any string is accepted | *
-matchtype | 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://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt 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 | Any string is accepted | *
-matchsense | 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 | Any integer value | 0 - any sense, 1 - forward sense, -1 - reverse sense
-minscore | If this is greater than or equal to the maximum score, then any score is permitted | Any numeric value | 0.0
-maxscore | If this is less than or equal to the maximum score, then any score is permitted | Any numeric value | 0.0
-matchtag | 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 | Any string is accepted | *
-matchvalue | 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 valueyou 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 | Any string is accepted | *
-stricttags | 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. | Boolean value Yes/No | No
Advanced (Unprompted) qualifiers | Allowed values | Default
-flatreformat | 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. | Boolean value Yes/No | No
-mincuts | 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. | Integer from 1 to 1000 | 1
-maxcuts | 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. | Integer up to 2000000000 | 2000000000
-sitelen | This sets the minimum length of the restriction enzyme recognition site. Any enzymes with sites shorter than this will be ignored. | Integer from 2 to 20 | 4
-single | 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. | Boolean value Yes/No | No
-[no]blunt | This allows those enzymes which cut at the same position on the forward and reverse strands to be considered. | Boolean value Yes/No | Yes
-[no]sticky | This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered. | Boolean value Yes/No | Yes
-[no]ambiguity | This allows those enzymes which have one or more 'N' ambiguity codes in their pattern to be considered | Boolean value Yes/No | Yes
-plasmid | If this is set then this allows searches for restriction enzyme recognition site and cut postions that span the end of the sequence to be considered. | Boolean value Yes/No | No
-[no]commercial | If this is set, then only those enzymes with a commercial supplier will be searched for. 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. 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. | Boolean value Yes/No | Yes
-[no]limit | 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. | Boolean value Yes/No | Yes
-orfminsize | 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. | Integer 0 or more | 0
-threeletter | Display protein sequences in three-letter code | Boolean value Yes/No | No
-number | Number the sequences | Boolean value Yes/No | No
-width | Width of sequence to display | Integer 1 or more | 60
-length | Line length of page (0 for indefinite) | Integer 0 or more | 0
-margin | Margin around sequence for numbering | Integer 0 or more | 10
-[no]name | Set this to be false if you do not wish to display the ID name of the sequence | Boolean value Yes/No | Yes
-[no]description | Set this to be false if you do not wish to display the description of the sequence | Boolean value Yes/No | Yes
-offset | Offset to start numbering the sequence from | Any integer value | 1
-html | Use HTML formatting | Boolean value Yes/No | No

## Input file format

showseq reads normal sequence USAs.

### Input files for usage example

'tembl:x13776' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:x13776

    ID   X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP.
    XX
    AC   X13776; M43175;
    XX
    DT   19-APR-1989 (Rel. 19, Created)
    DT   14-NOV-2006 (Rel. 89, Last updated, Version 24)
    XX
    DE   Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
    XX
    KW   aliphatic amidase regulator; amiC gene; amiR gene.
    XX
    OS   Pseudomonas aeruginosa
    OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
    OC   Pseudomonadaceae; Pseudomonas.
    XX
    RN   [1]
    RP   1167-2167
    RA   Rice P.M.;
    RT   ;
    RL   Submitted (16-DEC-1988) to the EMBL/GenBank/DDBJ databases.
    RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
    XX
    RN   [2]
    RP   1167-2167
    RX   DOI; 10.1016/0014-5793(89)80249-2.
    RX   PUBMED; 2495988.
    RA   Lowe N., Rice P.M., Drew R.E.;
    RT   "Nucleotide sequence of the aliphatic amidase regulator gene of Pseudomonas
    RT   aeruginosa";
    RL   FEBS Lett. 246(1-2):39-43(1989).
    XX
    RN   [3]
    RP   1-1292
    RX   PUBMED; 1907262.
    RA   Wilson S., Drew R.;
    RT   "Cloning and DNA seqence of amiC, a new gene regulating expression of the
    RT   Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
    RT   product.";
    RL   J. Bacteriol. 173(16):4914-4921(1991).
    XX
    RN   [4]
    RP   1-2167
    RA   Rice P.M.;
    RT   ;
    RL   Submitted (04-SEP-1991) to the EMBL/GenBank/DDBJ databases.
    RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
    XX
    DR   GOA; Q51417.
    DR   UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.
    XX

      [Part of this file has been deleted for brevity]

    FT                   /replace=""
    FT                   /note="ClaI fragment deleted in pSW36,  constitutive
    FT                   phenotype"
    FT   misc_feature    1
    FT                   /note="last base of an XhoI site"
    FT   misc_feature    648..653
    FT                   /note="end of 658bp XhoI fragment, deletion in  pSW3 causes
    FT                   constitutive expression of amiE"
    FT   conflict        1281
    FT                   /replace="g"
    FT                   /citation=[3]
    XX
    SQ   Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
         ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat        60
         ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       120
         aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       180
         aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       240
         agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       300
         ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       360
         tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       420
         agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       480
         acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       540
         ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       600
         gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       660
         acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       720
         cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       780
         ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       840
         aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt       900
         acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct       960
         tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc      1020
         tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt      1080
         acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca      1140
         gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc      1200
         agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt      1260
         ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg      1320
         cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca      1380
         gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt      1440
         gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc      1500
         gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc      1560
         cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga      1620
         tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa      1680
         gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca      1740
         ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct      1800
         gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg      1860
         aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt      1920
         catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg      1980
         gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct      2040
         gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa      2100
         ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt      2160
         cctcgag                                                                2167
    //

### Input files for usage example 4

'tsw:rs24_fugru' is a sequence entry in the example protein database 'tsw'

### Database entry: tsw:rs24_fugru

    ID   RS24_FUGRU              Reviewed;         132 AA.
    AC   O42387;
    DT   15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
    DT   01-JAN-1998, sequence version 1.
    DT   20-MAR-2007, entry version 25.
    DE   40S ribosomal protein S24.
    GN   Name=RPS24;
    OS   Fugu rubripes (Japanese pufferfish) (Takifugu rubripes).
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
    OC   Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei;
    OC   Acanthomorpha; Acanthopterygii; Percomorpha; Tetraodontiformes;
    OC   Tetradontoidea; Tetraodontidae; Takifugu.
    OX   NCBI_TaxID=31033;
    RN   [1]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    RA   Crosio C., Cecconi F., Giorgi M., Amaldi F., Mariottini P.;
    RL   Submitted (SEP-1997) to the EMBL/GenBank/DDBJ databases.
    CC   -!- SIMILARITY: Belongs to the ribosomal protein S24e family.
    CC   -----------------------------------------------------------------------
    CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
    CC   Distributed under the Creative Commons Attribution-NoDerivs License
    CC   -----------------------------------------------------------------------
    DR   EMBL; AJ001398; CAA04728.1; -; Genomic_DNA.
    DR   Ensembl; NEWSINFRUG00000143641; Fugu rubripes.
    DR   LinkHub; O42387; -.
    DR   InterPro; IPR001976; Ribosomal_S24E.
    DR   PANTHER; PTHR10496; Ribosomal_S24E; 1.
    DR   Pfam; PF01282; Ribosomal_S24e; 1.
    DR   ProDom; PD006052; Ribosomal_S24E; 1.
    DR   PROSITE; PS00529; RIBOSOMAL_S24E; 1.
    KW   Ribonucleoprotein; Ribosomal protein.
    FT   CHAIN         1    132       40S ribosomal protein S24.
    FT                                /FTId=PRO_0000137627.
    SQ   SEQUENCE   132 AA;  15305 MW;  DC437F60F20C14F5 CRC64;
         MNDTVTVRTR KFMTNRLLQR KQMVVDVLHP GKATVPKTEI REKLAKMYKT TPDVVFVFGF
         RTQFGGGKTT GFAMVYDSLD YAKKNEPKHR LARHGLFEKK KTSRKQRKER KNRMKKVRGT
         KKASVGASKK KD
    //

You can specifiy a file of ranges to display in uppercase by giving the '-uppercase' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-upper @myfile').

The format of the range file is:

- Comment lines start with '#' in the first column.
- Comment lines and blank lines are ignored.
- The line may start with white-space.
- There are two positive (integer) numbers per line separated by one or more space or
- TAB characters.
- The second number must be greater or equal to the first number.
- There can be optional text after the two numbers to annotate the line.
- White-space before or after the text is removed.

An example range file is:

    # this is my set of ranges
    12   23
     4   5       this is like 12-23, but smaller
    67   10348   interesting region

You can specifiy a file of ranges to highlight in a different colour when outputting in HTML format (using the '-html' qualifier) by giving the '-highlight' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-highlight @myfile').

The format of this file is very similar to the format of the above uppercase range file, except that the text after the start and end positions is used as the HTML colour name. This colour name is used 'as is' when specifying the colour in HTML in a '' construct, (where 'xxx' is the name of the colour).

The standard names of HTML font colours are given in:
http://http://www.w3.org/TR/REC-html40/types.html and http://www.ausmall.com.au/freegraf/ncolour2.htm and http://mindprod.com/htmlcolours.html (amongst other places).

An example highlight range file is:

    # this is my set of ranges
    12   23         red
     4   5          darkturquoise
    67   10348      #FFE4E1

You can specifiy a file of ranges to annotate by giving the '-annotate' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-annotate @myfile').

The format of this file is very similar to the format of the above highlight range file, except that the text after the start and end positions is used as the displayed text of the annotated region.

An example annotation range file is:

    # this is my set of ranges
    12   23         exon 1
     4   5          CAP site
    67   10348      exon 2

You can specify a file of enzyme names to read in by giving the '-enzymes' qualifier 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 '#' or '!' character 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, ppiI
    # other enzymes
    hindiii
    HinfI

## Output file format

### Output files for usage example

Note that although we asked for the sequence display to end at position '100', it has displayed the sequence up to the end of the line - position '120'. This is a feature of this program to make the display of things like restriction enzyme cutting sites easier.

### File: x13776.showseq

    X13776
    Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
    regulation

                       10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
              ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat
                     |===============|
                     promoter note="proposed rpoN-dependent promoter"
              |
              misc_feature note="last base of an XhoI site"

                       70        80        90        100
              ----:----|----:----|----:----|----:----|
              ctacctggcgagcctggagcacgagcgggttcgcttcgta
                  |===============|
              promoter note="proposed rpoN-dependent promoter"

### Output files for usage example 2

### File: x13776.showseq

    X13776
    Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
    regulation

              ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat
              ----:----|----:----|----:----|----:----|----:----|----:----|
              ccatggcgaccggctcgtagacgagctagtggtggtcggcccgctgcccttgacgtgcta

              ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac
              ----:----|----:----|----:----|----:----|----:----|----:----|
              gatggaccgctcggacctcgtgctcgcccaagcgaagcatgccgcgactcgctgtcagtg

### Output files for usage example 3

### File: x13776.showseq

              ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat
              ctacctggcgagcctggagcacgagcgggttcgcttcgta

### Output files for usage example 4

### File: rs24_fugru.showseq

    RS24_FUGRU
    40S ribosomal protein S24.

                       10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
              MAATVTVATALPMTAALLGALGMVVAVLHPGLATVPLTGIAGLLALMTLTTPAVVPVPGP
              esshaharhryhehsreelryleaasaeirlylharyhllrlyelyeyyhhrsaahahlh
              tnprlrlgrgsetrnguungsntllplusoysarlosruegusuastrsrroplleleye
              |===========================================================
              chain ftid="PRO_0000137627" note="40S ribosomal protein S24"

                       70        80        90        100       110       120
              ----:----|----:----|----:----|----:----|----:----|----:----|
              ATGPGGGLTTGPAMVTASLATALLAGPLHALAAHGLPGLLLTSALGALGALAAMLLVAGT
              rhlhlllyhhlhleayseesylyyslryirelrilehlyyyherylrylrysreyyarlh
              grneyyysrryeatlrpruprassnuossguagsyueusssrrgsngsugsngtsslgyr
              ============================================================
              chain ftid="PRO_0000137627" note="40S ribosomal protein S24"

                       130
              ----:----|--
              LLASVGASLLLA
              yylealleyyys
              ssarlyarsssp
              ===========|
              chain ftid="PRO_0000137627" note="40S ribosomal protein S24"

### Output files for usage example 5

### File: x13776.showseq

    X13776
    Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
    regulation
            1 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat 60
           61 ctacctggcgagcctggagcacgagcgggttcgcttcgta 100

### Output files for usage example 6

### File: x13776.showseq

    X13776
    Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
    regulation
          123 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat 182
          183 ctacctggcgagcctggagcacgagcgggttcgcttcgta 222

### Output files for usage example 7

### File: x13776.showseq

    X13776
    Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
    regulation
              ggtaccgctggccgagcatctgctCGATCACCACCAGCCGGGCGAcgggaactgcacgat
              ctacctggcgagcctggagcacgagcgggttcgcttcgta

### Output files for usage example 8

### File: x13776.showseq

    X13776
    Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
    regulation

                       10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
              ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat

                                      R  S  P  P  A  G  R  R  V
                     |===============|
                     promoter note="proposed rpoN-dependent promoter"
              |
              misc_feature note="last base of an XhoI site"

                       70        80        90        100       110       120
              ----:----|----:----|----:----|----:----|----:----|----:----|
              ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac

                     A  S  L
                  |===============|
                  promoter note="proposed rpoN-dependent promoter"

### Output files for usage example 9

### File: x13776.showseq

    X13776
    Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
    regulation

                       10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
              ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat
                          |------------|
                          binding site
                            |
                            SNP
                     |===============|
                     promoter note="proposed rpoN-dependent promoter"
              |
              misc_feature note="last base of an XhoI site"

                       70        80        90        100       110       120
              ----:----|----:----|----:----|----:----|----:----|----:----|
              ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac
                  |===============|
                  promoter note="proposed rpoN-dependent promoter"

Most of the variants of the output format have already been described in the 'Description' and 'Usage' sections, but here is some more just to fill out this section ;-)

The output format is extremely variable and under the control of the qualifiers used.

The sequence can be formatted for HTML display by using the '-html' qualifier. The top and tail html tags <HEAD>, <BODY> etc. are not included as it is expected that the output of this program will be included in a more extensive HTML page and so these parts are left to the user to provide.

The name of the sequence is displayed, followed by the description of the sequence. These can be turned off with the '-noname' and '-nodescription' qualifiers.

Then the sequence is output, one line at a time. Any associated information to be displayed is also output above and below the sequence line, as specified by the '-format' and or '-things' qualifiers. (See the 'Description' section for detals).

The margins around the sequence are specified by the use of the '-margin' qaulifier and any numbering of the sequence and its translations are placed in the margin.

A display of the restriction enzyme cut sites can be selected via '-format 6' option or the '-format 0 -thing b,r,s,-r' style of options.

The option '-format 7' will produce a formatted display of cut sites on the sequence, with the six-frame translation below it. The cut sites are indicated by a slash character '\' that points to the poition between the nucleotides where the cuts occur. Cuts by many enzymes at the same position are indicated by stacking the enzyme names on top of each other.

At the end the section header 'Enzymes that cut' is displayed followed by a list of the enzymes that cut the specified sequence and the number of times that they cut.

The '-flatreformat' qualifier changes the display to emphasise the recognition site of the restriction enzyme, which is indicated by a row of '=' characters. The cut site if pointed to by a '>' or '<' character and if the cut site is not within or imemdiately adjacent to the recognition site, they are linked by a row or '.' characters.

The name of the enzyme is displayed above (or below when the reverse sense site if displayed) the recognition site. The name of the enzyme is also displayed above the cut site if this occurs on a different display line to the recognition site (i.e. if it wraps onto the next line of sequence).

## Data files

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

The Genetic Code data files are based on the NCBI genetic code tables. Their names and descriptions are:

EGC.0
  Standard (Differs from GC.1 in that it only has initiation site 'AUG')
EGC.1
  Standard
EGC.2
  Vertebrate Mitochodrial
EGC.3
  Yeast Mitochondrial
EGC.4
  Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
EGC.5
  Invertebrate Mitochondrial
EGC.6
  Ciliate Macronuclear and Dasycladacean
EGC.9
  Echinoderm Mitochondrial
EGC.10
  Euplotid Nuclear
EGC.11
  Bacterial
EGC.12
  Alternative Yeast Nuclear
EGC.13
  Ascidian Mitochondrial
EGC.14
  Flatworm Mitochondrial
EGC.15
  Blepharisma Macronuclear
EGC.16
  Chlorophycean Mitochondrial
EGC.21
  Trematode Mitochondrial
EGC.22
  Scenedesmus obliquus
EGC.23
  Thraustochytrium Mitochondrial

The format of these files is very simple.

It consists of several lines of optional comments, each starting with a '#' character.

These are followed the line: 'Genetic Code [n]', where 'n' is the number of the genetic code file.

This is followed by the description of the code and then by four lines giving the IUPAC one-letter code of the translated amino acid, the start codons (indicdated by an 'M') and the three bases of the codon, lined up one on top of the other.

For example:

    ------------------------------------------------------------------------------
    # Genetic Code Table
    #
    # Obtained from: http://www.ncbi.nlm.nih.gov/collab/FT/genetic_codes.html
    # and: http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c
    #
    # Differs from Genetic Code [1] only in that the initiation sites have been
    # changed to only 'AUG'

    Genetic Code [0]
    Standard

    AAs  =   FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
    Starts = -----------------------------------M----------------------------
    Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
    ------------------------------------------------------------------------------

The EMBOSS REBASE restriction enzyme data files are stored iin directory 'data/REBASE/*' under the EMBOSS installation directory.

These files must first be set up using the program 'rebaseextract'. Running 'rebaseextract' may be the job of your system manager.

The data files are stored in the REBASE directory of the standard EMBOSS data directory. The names are:

- embossre.enz Cleavage information
- embossre.ref Reference/methylation information
- embossre.sup Supplier information

The column information is described at the top of the data files

The reported enzyme from any one group of isoschizomers (the prototype) is specified in the REBASE database and the information is held in the data file 'embossre.equ'. You may edit this file to set your own preferred prototype, if you wish.

The format of the file "embossre.equ" is
Enzyme-name Prototype-name

i.e. two columns of enzyme names separated by a space. The first name of the pair of enzymes is the name that is not preferred and the second is the preferred (prototype) name.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None known.

If you ask for the sequence display to end at position '100', with the qualifier '-send 100', it will display the sequence up to the end of the line - position '120'. This is a feature of this program to make the display of things like restriction enzyme cutting sites easier.

It is not a bug. Please don't report it.

## See also

Program name | Description
--- | ---
abiview | Reads ABI file and display the trace
backtranambig | Back translate a protein sequence to ambiguous codons
backtranseq | Back translate a protein sequence
cirdna | Draws circular maps of DNA constructs
coderet | Extract CDS, mRNA and translations from feature tables
lindna | Draws linear maps of DNA constructs
pepnet | Displays proteins as a helical net
pepwheel | Shows protein sequences as helices
plotorf | Plot potential open reading frames
prettyplot | Displays aligned sequences, with colouring and boxing
prettyseq | Output sequence with translated ranges
recoder | Remove restriction sites but maintain same translation
redata | Search REBASE for enzyme name, references, suppliers etc
remap | Display sequence with restriction sites, translation etc
restover | Find restriction enzymes producing specific overhang
restrict | Finds restriction enzyme cleavage sites
seealso | Finds programs sharing group names
showalign | Displays a multiple sequence alignment
showdb | Displays information on the currently available databases
showfeat | Show features of a sequence
showorf | Pretty output of DNA translations
silent | Silent mutation restriction enzyme scan
sixpack | Display a DNA sequence with 6-frame translation and ORFs
textsearch | Search sequence documentation. Slow, use SRS and Entrez!
transeq | Translate nucleic acid sequences

## Author(s)

Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

## History

Written 1999 - GWW
23 Aug 2000 - features display added - GWW
20 Nov 2001 - feature matches and annotation display added - GWW

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

None