File: showpep.html

package info (click to toggle)
emboss 6.6.0%2Bdfsg-1
links: PTS, VCS
area: main
in suites: jessie, jessie-kfreebsd
size: 571,248 kB
ctags: 39,971
sloc: ansic: 460,578; java: 29,439; perl: 13,573; sh: 12,740; makefile: 3,275; csh: 706; asm: 351; xml: 239; pascal: 237; modula3: 8
file content (1828 lines) | stat: -rw-r--r-- 59,112 bytes
parent folder | download | duplicates (6)
<HTML>

<HEAD>
  <TITLE>
  EMBOSS: showpep
  </TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">

<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
showpep
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Display protein sequences with features in pretty format
<H2>
    Description
</H2>

<p><b>showpep</b> displays one or more protein 
sequences, with features, in a style suitable for publication. The
output is sent to screen by default but can be written to file. You
may pick a format from a list, alternatively, use the many options to
control what is output and in what format. Optionally, the sequence
feature table can be displayed. There are various other
options for controlling how the sequence is displayed and numbered and
the output can be formatted for HTML.</p>


<H2>
    Usage
</H2>
Here is a sample session with <b>showpep</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>showpep tsw:laci_ecoli -sbeg 1 -send 100 </b>
Display protein sequences with features in pretty format
Things to display
         0 : Enter your own list of things to display
         1 : Sequence only
         2 : Default sequence with features
         3 : Pretty sequence 4:Baroque
Display format [2]: <b></b>
Output file [laci_ecoli.showpep]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<p>
<b>Example 2</b>
<p>
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,t,s', we will output the sequence in the following way: 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>showpep tsw:laci_ecoli -sbeg 1 -send 120 </b>
Display protein sequences with features in pretty format
Things to display
         0 : Enter your own list of things to display
         1 : Sequence only
         2 : Default sequence with features
         3 : Pretty sequence 4:Baroque
Display format [2]: <b>0</b>
Specify your own things to display
         S : Sequence
         B : Blank line
         T : Ticks line
         N : Number ticks line
         F : Features
         A : Annotation
Enter a list of things to display [B,N,T,S,A,F]: <b>b,t,s</b>
Output file [laci_ecoli.showpep]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#output.2">Go to the output files for this example</a><p><p>
<p>
<b>Example 3</b>
<p>
Display only the sequence: 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>showpep tsw:laci_ecoli -sbeg 1 -send 100 -noname -nodesc -format 0 -thing S </b>
Display protein sequences with features in pretty format
Output file [laci_ecoli.showpep]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#output.3">Go to the output files for this example</a><p><p>
<p>
<b>Example 4</b>
<p>
Protein sequence can be displayed in three-letter codes. (The codes are displayed downwards, so the first code is 'Met'):  
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>showpep tsw:rs24_takru -three -format 2 </b>
Display protein sequences with features in pretty format
Output file [rs24_takru.showpep]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#input.4">Go to the input files for this example</a><br><a href="#output.4">Go to the output files for this example</a><p><p>
<p>
<b>Example 5</b>
<p>
Number the sequence lines in the margin:  
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>showpep tsw:laci_ecoli -sbeg 1 -send 100 -format 1 -number </b>
Display protein sequences with features in pretty format
Output file [laci_ecoli.showpep]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#output.5">Go to the output files for this example</a><p><p>
<p>
<b>Example 6</b>
<p>
Start the numbering at a specified value ('123' in this case): 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>showpep tsw:laci_ecoli -sbeg 1 -send 100 -format 1 -number -offset 123 </b>
Display protein sequences with features in pretty format
Output file [laci_ecoli.showpep]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#output.6">Go to the output files for this example</a><p><p>
<p>
<b>Example 7</b>
<p>
Make selected regions uppercase. (Use '-slower' to force the rest of the sequence to be lowercase).  
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>showpep tsw:laci_ecoli -sbeg 1 -send 100 -format 1 -slower -upper "17-17,22-22" </b>
Display protein sequences with features in pretty format
Output file [laci_ecoli.showpep]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#output.7">Go to the output files for this example</a><p><p>
<p>
<b>Example 8</b>
<p>
Add your own annotation to the display: 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>showpep tsw:laci_ecoli -sbeg 1 -send 100 -format 2 -send 120 -annotation "6-25 binding site 17-17 SNP 22-22 SNP" </b>
Display protein sequences with features in pretty format
Output file [laci_ecoli.showpep]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#output.8">Go to the output files for this example</a><p><p>

<H2>
    Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Display protein sequences with features in pretty format
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqall     (Gapped) protein 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: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, ticks line, blank line; then you
                                  should enter 'S,T,B'. (Values: S (Sequence);
                                  B (Blank line); T (Ticks line); N (Number
                                  ticks line); F (Features); A (Annotation))
  [-outfile]           outfile    [*.showpep] Output file name

   Additional (Optional) qualifiers:
   -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'.
   -sourcematch        string     [*] By default any feature source in the
                                  feature table is shown. You can set this to
                                  match any feature source you wish to show.
                                  The source name is usually either the name
                                  of the program that detected the feature or
                                  it is the feature table (eg: EMBL) that the
                                  feature came from.
                                  The source may be wildcarded by using '*'.
                                  If you wish to show more than one source,
                                  separate their names with the character '|',
                                  eg:
                                  gene* | embl (Any string)
   -typematch          string     [*] By default any feature type in the
                                  feature table is shown. You can set this to
                                  match any feature type you wish to show.
                                  See http://www.ebi.ac.uk/embl/WebFeat/ for a
                                  list of the EMBL feature types and see
                                  Appendix A of the Swissprot user manual in
                                  http://www.expasy.org/sprot/userman.html for
                                  a list of the Swissprot feature types.
                                  The type may be wildcarded by using '*'.
                                  If you wish to show more than one type,
                                  separate their names with the character '|',
                                  eg:
                                  *UTR | intron (Any string)
   -minscore           float      [0.0] Minimum score of feature to display
                                  (see also maxscore) (Any numeric value)
   -maxscore           float      [0.0] Maximum score of feature to display.
                                  If both minscore and maxscore are zero (the
                                  default), then any score is ignored (Any
                                  numeric value)
   -tagmatch           string     [*] Tags are the types of extra values that
                                  a feature may have. 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)
   -valuematch         string     [*] Tag values are the values associated
                                  with a feature tag. Tags are the types of
                                  extra values that a feature may have. By
                                  default any feature tag value in the feature
                                  table is shown. You can set this to match
                                  any feature tag value you wish to show.
                                  The tag value may be wildcarded by using
                                  '*'.
                                  If you wish to show more than one tag value,
                                  separate their names with the character
                                  '|', eg:
                                  pax* | 10 (Any string)
   -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:
   -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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit

</pre>
</td></tr></table>
<P>

<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-sequence]<br>(Parameter 1)</td>
<td>seqall</td>
<td>(Gapped) protein sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-format</td>
<td>list</td>
<td>Display format</td>
<td><table><tr><td>0</td> <td><i>(Enter your own list of things to display)</i></td></tr><tr><td>1</td> <td><i>(Sequence only)</i></td></tr><tr><td>2</td> <td><i>(Default sequence with features)</i></td></tr><tr><td>3</td> <td><i>(Pretty sequence 4:Baroque)</i></td></tr></table></td>
<td>2</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-things</td>
<td>list</td>
<td>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, ticks line, blank line; then you should enter 'S,T,B'.</td>
<td><table><tr><td>S</td> <td><i>(Sequence)</i></td></tr><tr><td>B</td> <td><i>(Blank line)</i></td></tr><tr><td>T</td> <td><i>(Ticks line)</i></td></tr><tr><td>N</td> <td><i>(Number ticks line)</i></td></tr><tr><td>F</td> <td><i>(Features)</i></td></tr><tr><td>A</td> <td><i>(Annotation)</i></td></tr></table></td>
<td>B,N,T,S,A,F</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-outfile]<br>(Parameter 2)</td>
<td>outfile</td>
<td>Output file name</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.showpep</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-uppercase</td>
<td>range</td>
<td>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</td>
<td>Sequence range</td>
<td>If this is left blank, then the sequence case is left alone.</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-highlight</td>
<td>range</td>
<td>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'.</td>
<td>Sequence range</td>
<td><i>full sequence</i></td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-annotation</td>
<td>range</td>
<td>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'.</td>
<td>Sequence range</td>
<td>If this is left blank, then no annotation is added.</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-sourcematch</td>
<td>string</td>
<td>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</td>
<td>Any string</td>
<td>*</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-typematch</td>
<td>string</td>
<td>By default any feature type in the feature table is shown. You can set this to match any feature type you wish to show.
See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature types.
The type may be wildcarded by using '*'.
If you wish to show more than one type, separate their names with the character '|', eg:
*UTR | intron</td>
<td>Any string</td>
<td>*</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-minscore</td>
<td>float</td>
<td>Minimum score of feature to display (see also maxscore)</td>
<td>Any numeric value</td>
<td>0.0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-maxscore</td>
<td>float</td>
<td>Maximum score of feature to display.
If both minscore and maxscore are zero (the default), then any score is ignored</td>
<td>Any numeric value</td>
<td>0.0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-tagmatch</td>
<td>string</td>
<td>Tags are the types of extra values that a feature may have. 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</td>
<td>Any string</td>
<td>*</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-valuematch</td>
<td>string</td>
<td>Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. By default any feature tag value in the feature table is shown. You can set this to match any feature tag value you wish to show.
The tag value may be wildcarded by using '*'.
If you wish to show more than one tag value, separate their names with the character '|', eg:
pax* | 10</td>
<td>Any string</td>
<td>*</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-stricttags</td>
<td>boolean</td>
<td>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.</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-threeletter</td>
<td>boolean</td>
<td>Display protein sequences in three-letter code</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-number</td>
<td>boolean</td>
<td>Number the sequences</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-width</td>
<td>integer</td>
<td>Width of sequence to display</td>
<td>Integer 1 or more</td>
<td>60</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-length</td>
<td>integer</td>
<td>Line length of page (0 for indefinite)</td>
<td>Integer 0 or more</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-margin</td>
<td>integer</td>
<td>Margin around sequence for numbering</td>
<td>Integer 0 or more</td>
<td>10</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]name</td>
<td>boolean</td>
<td>Set this to be false if you do not wish to display the ID name of the sequence</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]description</td>
<td>boolean</td>
<td>Set this to be false if you do not wish to display the description of the sequence</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-offset</td>
<td>integer</td>
<td>Offset to start numbering the sequence from</td>
<td>Any integer value</td>
<td>1</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-html</td>
<td>boolean</td>
<td>Use HTML formatting</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-sequence" associated seqall qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sbegin1<br>-sbegin_sequence</td>
<td>integer</td>
<td>Start of each sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -send1<br>-send_sequence</td>
<td>integer</td>
<td>End of each sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sreverse1<br>-sreverse_sequence</td>
<td>boolean</td>
<td>Reverse (if DNA)</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sask1<br>-sask_sequence</td>
<td>boolean</td>
<td>Ask for begin/end/reverse</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -snucleotide1<br>-snucleotide_sequence</td>
<td>boolean</td>
<td>Sequence is nucleotide</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sprotein1<br>-sprotein_sequence</td>
<td>boolean</td>
<td>Sequence is protein</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -slower1<br>-slower_sequence</td>
<td>boolean</td>
<td>Make lower case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -supper1<br>-supper_sequence</td>
<td>boolean</td>
<td>Make upper case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -scircular1<br>-scircular_sequence</td>
<td>boolean</td>
<td>Sequence is circular</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -squick1<br>-squick_sequence</td>
<td>boolean</td>
<td>Read id and sequence only</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sformat1<br>-sformat_sequence</td>
<td>string</td>
<td>Input sequence format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -iquery1<br>-iquery_sequence</td>
<td>string</td>
<td>Input query fields or ID list</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ioffset1<br>-ioffset_sequence</td>
<td>integer</td>
<td>Input start position offset</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sdbname1<br>-sdbname_sequence</td>
<td>string</td>
<td>Database name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sid1<br>-sid_sequence</td>
<td>string</td>
<td>Entryname</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ufo1<br>-ufo_sequence</td>
<td>string</td>
<td>UFO features</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fformat1<br>-fformat_sequence</td>
<td>string</td>
<td>Features format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fopenfile1<br>-fopenfile_sequence</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outfile qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory2<br>-odirectory_outfile</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>


<H2>
    Input file format
</H2>

<b>showpep</b> reads one or more protein sequences.
<p>
<p>

The input is a standard EMBOSS sequence query (also known as a 'USA').

<p>
Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl

<p>

Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.

<p>
The input format can be specified by using the
command-line qualifier <tt>-sformat xxx</tt>, where 'xxx' is replaced
by the name of the required format.  The available format names are:
gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir
(nbrf), swissprot (swiss, sw), dasgff and debug.

<p>

See:
<A href="http://emboss.sf.net/docs/themes/SequenceFormats.html">
http://emboss.sf.net/docs/themes/SequenceFormats.html</A>
for further information on sequence formats.

<p>


<a name="input.1"></a>
<h3>Input files for usage example </h3>

'tsw:laci_ecoli' is a sequence entry in the example protein database 'tsw'
<p>
<p><h3>Database entry: tsw:laci_ecoli</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   LACI_ECOLI              Reviewed;         360 AA.
AC   P03023; O09196; P71309; Q2MC79; Q47338;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   19-JUL-2003, sequence version 3.
DT   13-JUN-2012, entry version 136.
DE   RecName: Full=Lactose operon repressor;
GN   Name=lacI; OrderedLocusNames=b0345, JW0336;
OS   Escherichia coli (strain K12).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=78246991; PubMed=355891; DOI=10.1038/274765a0;
RA   Farabaugh P.J.;
RT   "Sequence of the lacI gene.";
RL   Nature 274:765-769(1978).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Chen J., Matthews K.K.S.M.;
RL   Submitted (MAY-1991) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Marsh S.;
RL   Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RA   Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA   Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA   Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT   "Sequence of minutes 4-25 of Escherichia coli.";
RL   Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   MEDLINE=97426617; PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
RA   Mau B., Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1474(1997).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains


<font color=red>  [Part of this file has been deleted for brevity]</font>

FT   CHAIN         1    360       Lactose operon repressor.
FT                                /FTId=PRO_0000107963.
FT   DOMAIN        1     58       HTH lacI-type.
FT   DNA_BIND      6     25       H-T-H motif.
FT   VARIANT     282    282       Y -&gt; D (in T41 mutant).
FT   MUTAGEN      17     17       Y-&gt;H: Broadening of specificity.
FT   MUTAGEN      22     22       R-&gt;N: Recognizes an operator variant.
FT   CONFLICT    286    286       L -&gt; S (in Ref. 1, 4 and 7).
FT   HELIX         6     11
FT   TURN         12     14
FT   HELIX        17     24
FT   HELIX        33     45
FT   HELIX        51     56
FT   STRAND       63     69
FT   HELIX        74     89
FT   STRAND       93     98
FT   STRAND      101    103
FT   HELIX       104    115
FT   TURN        116    118
FT   STRAND      122    126
FT   HELIX       130    139
FT   TURN        140    142
FT   STRAND      145    150
FT   STRAND      154    156
FT   STRAND      158    161
FT   HELIX       163    177
FT   STRAND      181    186
FT   HELIX       192    207
FT   STRAND      213    217
FT   HELIX       222    234
FT   STRAND      240    246
FT   HELIX       247    259
FT   TURN        265    267
FT   STRAND      268    271
FT   HELIX       277    281
FT   STRAND      282    284
FT   STRAND      287    290
FT   HELIX       293    308
FT   STRAND      314    319
FT   STRAND      322    324
FT   STRAND      334    338
FT   HELIX       343    353
FT   HELIX       354    356
SQ   SEQUENCE   360 AA;  38590 MW;  347A8DEE92D736CB CRC64;
     MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RVAQQLAGKQ
     SLLIGVATSS LALHAPSQIV AAIKSRADQL GASVVVSMVE RSGVEACKAA VHNLLAQRVS
     GLIINYPLDD QDAIAVEAAC TNVPALFLDV SDQTPINSII FSHEDGTRLG VEHLVALGHQ
     QIALLAGPLS SVSARLRLAG WHKYLTRNQI QPIAEREGDW SAMSGFQQTM QMLNEGIVPT
     AMLVANDQMA LGAMRAITES GLRVGADISV VGYDDTEDSS CYIPPLTTIK QDFRLLGQTS
     VDRLLQLSQG QAVKGNQLLP VSLVKRKTTL APNTQTASPR ALADSLMQLA RQVSRLESGQ
//
</pre>
</td></tr></table><p>

<a name="input.4"></a>
<h3>Input files for usage example 4</h3>
<p><h3>Database entry: tsw:rs24_takru</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   RS24_TAKRU              Reviewed;         132 AA.
AC   O42387;
DT   15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT   01-JAN-1998, sequence version 1.
DT   16-MAY-2012, entry version 54.
DE   RecName: Full=40S ribosomal protein S24;
GN   Name=rps24;
OS   Takifugu rubripes (Japanese pufferfish) (Fugu 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   ProteinModelPortal; O42387; -.
DR   STRING; O42387; -.
DR   PRIDE; O42387; -.
DR   eggNOG; COG2004; -.
DR   InParanoid; O42387; -.
DR   GO; GO:0005840; C:ribosome; IEA:UniProtKB-KW.
DR   GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
DR   GO; GO:0003735; F:structural constituent of ribosome; IEA:InterPro.
DR   GO; GO:0006412; P:translation; IEA:InterPro.
DR   Gene3D; G3DSA:3.30.70.330; a_b_plait_nuc_bd; 1.
DR   InterPro; IPR012677; Nucleotide-bd_a/b_plait.
DR   InterPro; IPR012678; Ribosomal_L23/L15e_core_dom.
DR   InterPro; IPR001976; Ribosomal_S24e.
DR   InterPro; IPR018098; Ribosomal_S24e_CS.
DR   PANTHER; PTHR10496; Ribosomal_S24E; 1.
DR   Pfam; PF01282; Ribosomal_S24e; 1.
DR   ProDom; PD006052; Ribosomal_S24e; 1.
DR   SUPFAM; SSF54189; L23_L15e_core; 1.
DR   PROSITE; PS00529; RIBOSOMAL_S24E; 1.
PE   3: Inferred from homology;
KW   Complete proteome; Reference proteome; Ribonucleoprotein;
KW   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
//
</pre>
</td></tr></table><p>

<p>

You can specify 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').

<p>
          
The format of the range file is:

<p>

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

<p>

An example range file is:

<p>

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

<p>

You can specify 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').

<p>

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 '<FONT COLOR=xxx>'
construct, (where 'xxx' is the name of the colour).

<p>

The standard names of HTML font colours are given in
<A HREF="http://http://www.w3.org/TR/REC-html40/types.html#h-6.5">
http://http://www.w3.org/TR/REC-html40/types.html#h-6.5</A>


<p>

An example highlight range file is:

<p>

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

<p>

You can specify 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').

<p>
     
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.

<p>

An example annotation range file is:

<p>
   
<pre>
# this is my set of ranges
12   23         exon 1
 4   5          CAP site
67   10348      exon 2
</pre>

<p>



<H2>
    Output file format
</H2>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: laci_ecoli.showpep</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
LACI_ECOLI
Lactose operon repressor

                   10        20        30        40        50        60        
          ----:----|----:----|----:----|----:----|----:----|----:----|
          MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ
          |===========================================================
          mature_protein_region note="Lactose operon repressor" ftid="PRO_00001
          |========================================================|
          polypeptide_domain note="HTH lacI-type"
               |==================|                         |====|
               DNA_contact note="H-T-H motif"               alpha_helix
                          |
          mutated_variant_site note="Y-&gt;H: Broadening of specificity"
                               |
          mutated_variant_site note="R-&gt;N: Recognizes an operator variant"
               |====|                     |===========|
               alpha_helix                alpha_helix
                     |=|
                     polypeptide_turn_motif
                          |======|
                          alpha_helix

                   70        80        90        100       
          ----:----|----:----|----:----|----:----|
          SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE
          ========================================
          mature_protein_region note="Lactose operon repressor" ftid="PRO_00001
            |=====|                       |====|
            beta_strand                   beta_strand
                       |==============|
                       alpha_helix

</pre>
</td></tr></table><p>

<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: laci_ecoli.showpep</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
LACI_ECOLI
Lactose operon repressor

          ----:----|----:----|----:----|----:----|----:----|----:----|
          MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ

          ----:----|----:----|----:----|----:----|----:----|----:----|
          SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVS

</pre>
</td></tr></table><p>

<a name="output.3"></a>
<h3>Output files for usage example 3</h3>
<p><h3>File: laci_ecoli.showpep</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
          MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ
          SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE

</pre>
</td></tr></table><p>

<a name="output.4"></a>
<h3>Output files for usage example 4</h3>
<p><h3>File: rs24_takru.showpep</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
RS24_TAKRU
40S ribosomal protein S24

                   10        20        30        40        50        60        
          ----:----|----:----|----:----|----:----|----:----|----:----|
          MAATVTVATALPMTAALLGALGMVVAVLHPGLATVPLTGIAGLLALMTLTTPAVVPVPGP
          esshaharhryhehsreelryleaasaeirlylharyhllrlyelyeyyhhrsaahahlh
          tnprlrlgrgsetrnguungsntllplusoysarlosruegusuastrsrroplleleye
          |===========================================================
          mature_protein_region note="40S ribosomal protein S24" ftid="PRO_0000

                   70        80        90        100       110       120       
          ----:----|----:----|----:----|----:----|----:----|----:----|
          ATGPGGGLTTGPAMVTASLATALLAGPLHALAAHGLPGLLLTSALGALGALAAMLLVAGT
          rhlhlllyhhlhleayseesylyyslryirelrilehlyyyherylrylrysreyyarlh
          grneyyysrryeatlrpruprassnuossguagsyueusssrrgsngsugsngtsslgyr
          ============================================================
          mature_protein_region note="40S ribosomal protein S24" ftid="PRO_0000

                   130       
          ----:----|--
          LLASVGASLLLA
          yylealleyyys
          ssarlyarsssp
          ===========|
          mature_protein_region note="40S ribosomal protein S24" ftid="PRO_0000

</pre>
</td></tr></table><p>

<a name="output.5"></a>
<h3>Output files for usage example 5</h3>
<p><h3>File: laci_ecoli.showpep</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
LACI_ECOLI
Lactose operon repressor
        1 MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ 60
       61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE 100

</pre>
</td></tr></table><p>

<a name="output.6"></a>
<h3>Output files for usage example 6</h3>
<p><h3>File: laci_ecoli.showpep</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
LACI_ECOLI
Lactose operon repressor
      123 MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ 182
      183 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE 222

</pre>
</td></tr></table><p>

<a name="output.7"></a>
<h3>Output files for usage example 7</h3>
<p><h3>File: laci_ecoli.showpep</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
LACI_ECOLI
Lactose operon repressor
          mkpvtlydvaeyagvsYqtvsRvvnqashvsaktrekveaamaelnyipnrvaqqlagkq
          slligvatsslalhapsqivaaiksradqlgasvvvsmve

</pre>
</td></tr></table><p>

<a name="output.8"></a>
<h3>Output files for usage example 8</h3>
<p><h3>File: laci_ecoli.showpep</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
LACI_ECOLI
Lactose operon repressor

                   10        20        30        40        50        60        
          ----:----|----:----|----:----|----:----|----:----|----:----|
          MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ
               |------------------|
               binding site
                          |    |
                          SNP  SNP
          |===========================================================
          mature_protein_region note="Lactose operon repressor" ftid="PRO_00001
          |========================================================|
          polypeptide_domain note="HTH lacI-type"
               |==================|                         |====|
               DNA_contact note="H-T-H motif"               alpha_helix
                          |
          mutated_variant_site note="Y-&gt;H: Broadening of specificity"
                               |
          mutated_variant_site note="R-&gt;N: Recognizes an operator variant"
               |====|                     |===========|
               alpha_helix                alpha_helix
                     |=|
                     polypeptide_turn_motif
                          |======|
                          alpha_helix

                   70        80        90        100       110       120       
          ----:----|----:----|----:----|----:----|----:----|----:----|
          SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVS
          ============================================================
          mature_protein_region note="Lactose operon repressor" ftid="PRO_00001
            |=====|                       |====|
            beta_strand                   beta_strand
                       |==============|           |=|
                       alpha_helix                beta_strand
                                                     |==========|
                                                     alpha_helix
                                                                 |=|
                                              polypeptide_turn_motif

</pre>
</td></tr></table><p>

<p>

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.

<p>

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

<p>
          
The sequence can be formatted for HTML display by using the '-html'
qualifier.  The top and tail html tags &lt;HEAD&gt;, &lt;BODY&gt; 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.

<p>

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.

<p>
      
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).

<p>
          
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.




<H2>
    Data files
</H2>

<p>
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.

<p>

To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:

<pre>

% embossdata -fetch -file Exxx.dat

</pre>
<p>

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".

<p>
The directories are searched in the following order:

<ul>
   <li> . (your current directory)
   <li> .embossdata (under your current directory)
   <li> ~/ (your home directory)
   <li> ~/.embossdata
</ul>
<p>


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

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

<p>

The format of these files is very simple.

<p>   

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

<p>

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

<p> 

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.
   
<p>

For example:

<pre>
   
------------------------------------------------------------------------------
# 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
------------------------------------------------------------------------------

</pre>

<p>      
The EMBOSS REBASE restriction enzyme data files are stored in
directory 'data/REBASE/*' under the EMBOSS installation directory.

<p>

These files must first be set up using the program <a
href="rebaseextract.html">'<b>rebaseextract</b>'</a>.  Running
'rebaseextract' may be the job of your system manager.

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

<ul>
<li> embossre.enz     Cleavage information
<li> embossre.ref     Reference/methylation information
<li> embossre.sup     Supplier information
</ul>
	 
The column information is described at the top of the data files
	 
<p>
	 
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. 
	 
<p>
	 
The format of the file "embossre.equ" is
<br>
Enzyme-name Prototype-name
	 
<p>
	 
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. 
	 
	          

<H2>
    Notes
</H2>

<p>One or more things may be selected for display from a menu
(<tt>-things</tt> option).  The order of specified characters (upper
or lower case) determines the order in the output:</p>
<pre>
s	Sequence
b	Blank line
t	Ticks line
n	Number ticks line
f	Features (from the feature table or from a command line -ufo file)
a	User Annotation
</pre>

<p>Alternatively, there is a selection of pre-defined formats to
choose from. The codes from above used in the list of standard formats
are:</p>
<pre>
Sequence only:                  S A
Default sequence:               B N T S A F
Pretty sequence:                B N T S A
Baroque:                        B N T S T A F</pre>



<p>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 (<tt>b</tt>), then the position numbers of
the ticks (<tt>n</tt>) then the ticks every 10 characters (<tt>t</tt>)
then the sequence itself (<tt>s</tt>) then any user-supplied
annotation (<tt>a</tt>) then the features from the feature table
(<tt>f</tt>). Subsequent lines of the sequence output will repeat this
format.</p>

<p>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.</p>

<p>If the sequence is in SwissProt format, the
feature table of the sequence can be displayed with the sequence. GFF
file features can also be displayed if they are included on the
command line using <tt>-ufo=file</tt>.</p>

<p>
Other display options include: 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. An initial position to
start the numbering from can be set.  The width of a line, and width
of a margin around the sequence reserved for numbering can be set.
Specified regions of the sequence can be displayed in uppercase to
highlight them.</p>


<H2>
    References
</H2>

None.

<H2>
    Warnings
</H2>

None.

<H2>
    Diagnostic Error Messages
</H2>

None.

<H2>
    Exit status
</H2>

It always exits with status 0.

<H2>
    Known bugs
</H2>

None known.

<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th>
<th>Description</th></tr>
<tr>
<td><a href="abiview.html">abiview</a></td>
<td>Display the trace in an ABI sequencer file</td>
</tr>

<tr>
<td><a href="cirdna.html">cirdna</a></td>
<td>Draw circular map of DNA constructs</td>
</tr>

<tr>
<td><a href="iep.html">iep</a></td>
<td>Calculate the isoelectric point of proteins</td>
</tr>

<tr>
<td><a href="lindna.html">lindna</a></td>
<td>Draw linear maps of DNA constructs</td>
</tr>

<tr>
<td><a href="pepinfo.html">pepinfo</a></td>
<td>Plot amino acid properties of a protein sequence in parallel</td>
</tr>

<tr>
<td><a href="pepnet.html">pepnet</a></td>
<td>Draw a helical net for a protein sequence</td>
</tr>

<tr>
<td><a href="pepwheel.html">pepwheel</a></td>
<td>Draw a helical wheel diagram for a protein sequence</td>
</tr>

<tr>
<td><a href="plotorf.html">plotorf</a></td>
<td>Plot potential open reading frames in a nucleotide sequence</td>
</tr>

<tr>
<td><a href="prettyplot.html">prettyplot</a></td>
<td>Draw a sequence alignment with pretty formatting</td>
</tr>

<tr>
<td><a href="prettyseq.html">prettyseq</a></td>
<td>Write a nucleotide sequence and its translation to file</td>
</tr>

<tr>
<td><a href="remap.html">remap</a></td>
<td>Display restriction enzyme binding sites in a nucleotide sequence</td>
</tr>

<tr>
<td><a href="showfeat.html">showfeat</a></td>
<td>Display features of a sequence in pretty format</td>
</tr>

<tr>
<td><a href="sixpack.html">sixpack</a></td>
<td>Display a DNA sequence with 6-frame translation and ORFs</td>
</tr>

</table>

<H2>
    Author(s)
</H2>
Gary Williams formerly at:
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.


<H2>
    History
</H2>


<H2>
    Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.

<H2>
    Comments
</H2>
None

</BODY>
</HTML>