
                                  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:paamir -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 [paamir.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:paamir -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 [paamir.showseq]: 
   
   Go to the output files for this example
   
   Example 3
   
   Display only the sequence:
   

% showseq tembl:paamir -sbeg 1 -send 100 -noname -nodesc -format 0 -thing S 
Display a sequence with features, translation etc..
Output file [paamir.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:paamir -sbeg 1 -send 100 -format 1 -number 
Display a sequence with features, translation etc..
Output file [paamir.showseq]: 
   
   Go to the output files for this example
   
   Example 6
   
   Start the numbering at a specified value ('123' in this case):
   

% showseq tembl:paamir -sbeg 1 -send 100 -format 1 -number -offset 123 
Display a sequence with features, translation etc..
Output file [paamir.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:paamir -sbeg 1 -send 100 -format 1 -slower -upper '25-45,101-20
3,333-362' 
Display a sequence with features, translation etc..
Output file [paamir.showseq]: 
   
   Go to the output files for this example
   
   Example 8
   
   Translate selected regions:
   

% showseq tembl:paamir -sbeg 1 -send 120 -format 4 -trans 25-49,66-76 
Display a sequence with features, translation etc..
Output file [paamir.showseq]: 
   
   Go to the output files for this example
   
   Example 9
   
   Add your own annotation to the display:
   

% showseq tembl:paamir -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 [paamir.showseq]: 
   
   Go to the output files for this example
   
Command line arguments

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqall     Sequence database USA
   -format             menu       Display format
*  -things             menu       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'.
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers:
   -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
                                  1,5,8,10,23,45,57,99
   -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
   -table              menu       Genetic code to use
   -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
   -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
   -matchsense         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      If this is greater than or equal to the
                                  maximum score, then any score is permitted
   -maxscore           float      If this is less than or equal to the maximum
                                  score, then any score is permitted
   -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
   -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
   -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.

   Advanced (Unprompted) qualifiers:
   -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.
   -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.
   -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.
   -sitelen            integer    This sets the minimum length of the
                                  restriction enzyme recognition site. Any
                                  enzymes with sites shorter than this will be
                                  ignored.
   -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.
   -[no]blunt          boolean    This allows those enzymes which cut at the
                                  same position on the forward and reverse
                                  strands to be considered.
   -[no]sticky         boolean    This allows those enzymes which cut at
                                  different positions on the forward and
                                  reverse strands, leaving an overhang, to be
                                  considered.
   -[no]ambiguity      boolean    This allows those enzymes which have one or
                                  more 'N' ambiguity codes in their pattern to
                                  be considered
   -plasmid            boolean    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    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    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    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.
   -threeletter        boolean    Display protein sequences in three-letter
                                  code
   -number             boolean    Number the sequences
   -width              integer    Width of sequence to display
   -length             integer    Line length of page (0 for indefinite)
   -margin             integer    Margin around sequence for numbering
   -[no]name           boolean    Set this to be false if you do not wish to
                                  display the ID name of the sequence
   -[no]description    boolean    Set this to be false if you do not wish to
                                  display the description of the sequence
   -offset             integer    Offset to start numbering the sequence from
   -html               boolean    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 deaths
   

   Standard (Mandatory) qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database 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 <sequence>.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:paamir' is a sequence entry in the example nucleic acid
   database 'tembl'
   
  Database entry: tembl:paamir
  
ID   PAAMIR     standard; DNA; PRO; 2167 BP.
XX
AC   X13776; M43175;
XX
SV   X13776.1
XX
DT   19-APR-1989 (Rel. 19, Created)
DT   17-FEB-1997 (Rel. 50, Last updated, Version 22)
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; gamma subdivision; 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   MEDLINE; 89211409.
RA   Lowe N., Rice P.M., Drew R.E.;
RT   "Nucleotide sequence of the aliphatic amidase regulator gene of Pseudomona
s
RT   aeruginosa";
RL   FEBS Lett. 246:39-43(1989).
XX
RN   [3]
RP   1-1292
RX   MEDLINE; 91317707.
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. 173:4914-4921(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   SWISS-PROT; P10932; AMIR_PSEAE.
DR   SWISS-PROT; P27017; AMIC_PSEAE.
DR   SWISS-PROT; Q51417; AMIS_PSEAE.


  [Part of this file has been deleted for brevity]

FT                   phenotype"
FT                   /replace=""
FT                   /gene="amiC"
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 cause
s
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        6
0
     ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       12
0
     aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       18
0
     aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       24
0
     agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       30
0
     ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       36
0
     tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       42
0
     agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       48
0
     acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       54
0
     ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       60
0
     gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       66
0
     acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       72
0
     cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       78
0
     ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       84
0
     aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt       90
0
     acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct       96
0
     tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc      102
0
     tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt      108
0
     acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca      114
0
     gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc      120
0
     agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt      126
0
     ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg      132
0
     cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca      138
0
     gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt      144
0
     gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc      150
0
     gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc      156
0
     cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga      162
0
     tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa      168
0
     gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca      174
0
     ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct      180
0
     gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg      186
0
     aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt      192
0
     catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg      198
0
     gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct      204
0
     gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa      210
0
     ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt      216
0
     cctcgag                                                                216
7
//
   
  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     STANDARD;      PRT;   132 AA.
AC   O42387;
DT   15-JUL-1998 (REL. 36, CREATED)
DT   15-JUL-1998 (REL. 36, LAST SEQUENCE UPDATE)
DT   15-JUL-1998 (REL. 36, LAST ANNOTATION UPDATE)
DE   40S RIBOSOMAL PROTEIN S24.
GN   RPS24.
OS   FUGU RUBRIPES (JAPANESE PUFFERFISH) (TAKIFUGU RUBRIPES).
OC   EUKARYOTA; METAZOA; CHORDATA; VERTEBRATA; PISCES; GNATHOSTOMATA;
OC   OSTEICHTHYES; ACTINOPTERYGII; TETRAODONTIFORMES.
RN   [1]
RP   SEQUENCE FROM N.A.
RA   CROSIO C., CECCONI F., GIORGI M., AMALDI F., MARIOTTINI P.;
RL   SUBMITTED (SEP-1997) TO EMBL/GENBANK/DDBJ DATA BANKS.
CC   -!- SIMILARITY: BELONGS TO THE S24E FAMILY OF RIBOSOMAL PROTEINS.
DR   EMBL; AJ001398; E339629; -.
DR   PROSITE; PS00529; RIBOSOMAL_S24E; 1.
KW   RIBOSOMAL PROTEIN.
SQ   SEQUENCE   132 AA;  15305 MW;  BCF9EB31 CRC32;
     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: paamir.showseq
  
PAAMIR
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       110       120
          ----:----|----:----|----:----|----:----|----:----|----:----|
          ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac
              |===============|
              promoter note="proposed rpoN-dependent promoter"
   
  Output files for usage example 2
  
  File: paamir.showseq
  
PAAMIR
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation

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

          ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac
          ----:----|----:----|----:----|----:----|----:----|----:----|
          gatggaccgctcggacctcgtgctcgcccaagcgaagcatgccgcgactcgctgtcagtg
   
  Output files for usage example 3
  
  File: paamir.showseq
  
          ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat
          ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac
   
  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

                   70        80        90        100       110       120
          ----:----|----:----|----:----|----:----|----:----|----:----|
          ATGPGGGLTTGPAMVTASLATALLAGPLHALAAHGLPGLLLTSALGALGALAAMLLVAGT
          rhlhlllyhhlhleayseesylyyslryirelrilehlyyyherylrylrysreyyarlh
          grneyyysrryeatlrpruprassnuossguagsyueusssrrgsngsugsngtsslgyr

                   130       140       150       160       170       180
          ----:----|----:----|----:----|----:----|----:----|----:----|
          LLASVGASLLLA
          yylealleyyys
          ssarlyarsssp
   
  Output files for usage example 5
  
  File: paamir.showseq
  
PAAMIR
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation
        1 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat 60
       61 ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac 120
   
  Output files for usage example 6
  
  File: paamir.showseq
  
PAAMIR
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation
      123 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat 182
      183 ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac 242
   
  Output files for usage example 7
  
  File: paamir.showseq
  
PAAMIR
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation
          ggtaccgctggccgagcatctgctCGATCACCACCAGCCGGGCGAcgggaactgcacgat
          ctacctggcgagcctggagcacgagcgggttcgcttcgtaCGGCGCTGAGCGACAGTCAC
   
  Output files for usage example 8
  
  File: paamir.showseq
  
PAAMIR
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: paamir.showseq
  
PAAMIR
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 Mitochondrial
EGC.3      Yeast Mitochondrial
EGC.4      Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplas
ma
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

   showseq uses the EMBOSS REBASE data files in '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
   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
   recite Find changes to an enzyme site that introduce new enzyme sites
   recoder Remove restriction sites but maintain the same translation
   redata Search REBASE for enzyme name, references, suppliers etc
   remap Display a sequence with restriction cut sites, translation etc
   restover Finds restriction enzymes that produce a 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 text. SRS and Entrez are
   faster!
   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
