
                              EMBOSS: showfeat
     _________________________________________________________________
   
                               Program showfeat
                                       
Function

   Show features of a sequence
   
Description

   Showfeat reads a protein or nucleic sequence and its feature table,
   and writes a text representation of the features to standard output.
   
Usage

   Here is a sample session with showfeat. The feature table is specified
   as a -ufo qualifier (uniform feature object), in this case a file
   containing an EMBL feature table.

% showfeat -ufo paamir.ft
Show features of a sequence.
Input sequence(s): embl:paamir
Output file [stdout]:
PAAMIR
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
|==========================================================| 2167
|----------------------------------------------------------> source
>                                                            promoter
|>                                                           promoter
  >                                                          RBS
  |------------------------------->                          CDS
                |>                                           misc_feature
                        |------>                             mutation
                                  |---------------->         CDS
|                                                            misc_feature
                                  |                          conflict

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-outfile]           outfile    If you enter the name of a file here then
                                  this program will write the feature details
                                  into that file.

   Optional qualifiers:
   -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
   -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
   -sort               menu       Sort features by Type, Start or Source, or
                                  Nosort (don't sort - use input order)

   Advanced qualifiers:
   -html               bool       Use HTML formatting
   -[no]id             bool       Set this to be false if you do not wish to
                                  display the ID name of the sequence.
   -[no]description    bool       Set this to be false if you do not wish to
                                  display the description of the sequence.
   -[no]scale          bool       Set this to be false if you do not wish to
                                  display the scale line.
   -width              integer    You can expand (or contract) the width of
                                  the ASCII-character graphics display of the
                                  positions of the features using this value.
                                  For example, a width of 80 characters would
                                  cover a standard page width and a width a 10
                                  characters would be nearly unreadable.
                                  If the width is set to less than 4, the
                                  graphics lines and the scale line will not
                                  be displayed.
   -collapse           bool       If this is set, then features from the same
                                  source and of the same type and sense are
                                  all printed on the same line. For instance
                                  if there are several features from the EMBL
                                  feature table (ie. the same source) which
                                  are all of type 'exon' in the same sense,
                                  then they will all be displayed on the same
                                  line. This makes it hard to distinguish
                                  overlapping features.
                                  If this is set to false then each feature is
                                  displayed on a separate line making it
                                  easier to distinguish where features start
                                  and end.
   -[no]forward        bool       Set this to be false if you do not wish to
                                  display forward sense features.
   -[no]reverse        bool       Set this to be false if you do not wish to
                                  display reverse sense features.
   -[no]unknown        bool       Set this to be false if you do not wish to
                                  display unknown sense features. (ie.
                                  features with no directionality - all
                                  protein features are of this type and some
                                  nucleic features (for example, CG-rich
                                  regions)).
   -strand             bool       Set this if you wish to display the strand
                                  of the features. Protein features are always
                                  directionless (indicated by '0'), forward
                                  is indicated by '+' and reverse is '-'.
   -source             bool       Set this if you wish to display the source
                                  of the features.
                                  The source name is usually either the name
                                  of the program that detected the feature or
                                  it is the name of the feature table (eg:
                                  EMBL) that the feature came from.
   -position           bool       Set this if you wish to display the start
                                  and end position of the features. If several
                                  features are being displayed on the same
                                  line, then the start and end positions will
                                  be joined by a comma, for example:
                                  '189-189,225-225'.
   -[no]type           bool       Set this to be false if you do not wish to
                                  display the type of the features.
   -tags               bool       Set this to be false if you do not wish to
                                  display the tags and values of the features.
   -[no]values         bool       Set this to be false if you do not wish to
                                  display the tag values of the features. If
                                  this is set to be false, only the tag names
                                  will be displayed. If the tags are not
                                  displayed, then the values will not be
                                  displayed. The value of the 'translation'
                                  tag is never displayed as it is often
                                  extremely long.

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-outfile]
   (Parameter 2) If you enter the name of a file here then this program
   will write the feature details into that file. Output file stdout
   Optional qualifiers Allowed values Default
   -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 *
   -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 *
   -sort Sort features by Type, Start or Source, or Nosort (don't sort -
   use input order)
   source (Sort by Source)
   start  (Sort by Start position)
   type   (Sort by Type)
   nosort (No sorting done)
   start
   Advanced qualifiers Allowed values Default
   -html Use HTML formatting Yes/No No
   -[no]id Set this to be false if you do not wish to display the ID name
   of the sequence. Yes/No Yes
   -[no]description Set this to be false if you do not wish to display
   the description of the sequence. Yes/No Yes
   -[no]scale Set this to be false if you do not wish to display the
   scale line. Yes/No Yes
   -width You can expand (or contract) the width of the ASCII-character
   graphics display of the positions of the features using this value.
   For example, a width of 80 characters would cover a standard page
   width and a width a 10 characters would be nearly unreadable. If the
   width is set to less than 4, the graphics lines and the scale line
   will not be displayed. Integer 0 or more 60
   -collapse If this is set, then features from the same source and of
   the same type and sense are all printed on the same line. For instance
   if there are several features from the EMBL feature table (ie. the
   same source) which are all of type 'exon' in the same sense, then they
   will all be displayed on the same line. This makes it hard to
   distinguish overlapping features. If this is set to false then each
   feature is displayed on a separate line making it easier to
   distinguish where features start and end. Yes/No No
   -[no]forward Set this to be false if you do not wish to display
   forward sense features. Yes/No Yes
   -[no]reverse Set this to be false if you do not wish to display
   reverse sense features. Yes/No Yes
   -[no]unknown Set this to be false if you do not wish to display
   unknown sense features. (ie. features with no directionality - all
   protein features are of this type and some nucleic features (for
   example, CG-rich regions)). Yes/No Yes
   -strand Set this if you wish to display the strand of the features.
   Protein features are always directionless (indicated by '0'), forward
   is indicated by '+' and reverse is '-'. Yes/No No
   -source Set this if you wish to display the source of the features.
   The source name is usually either the name of the program that
   detected the feature or it is the name of the feature table (eg: EMBL)
   that the feature came from. Yes/No No
   -position Set this if you wish to display the start and end position
   of the features. If several features are being displayed on the same
   line, then the start and end positions will be joined by a comma, for
   example: '189-189,225-225'. Yes/No No
   -[no]type Set this to be false if you do not wish to display the type
   of the features. Yes/No Yes
   -tags Set this to be false if you do not wish to display the tags and
   values of the features. Yes/No No
   -[no]values Set this to be false if you do not wish to display the tag
   values of the features. If this is set to be false, only the tag names
   will be displayed. If the tags are not displayed, then the values will
   not be displayed. The value of the 'translation' tag is never
   displayed as it is often extremely long. Yes/No Yes
   
Input file format

   The feature input is the feature table lines from the database entry
   in EMBL format.
   
   Here is the file:

FH   Key             Location/Qualifiers
FH
FT   source          1..2167
FT                   /db_xref="taxon:287"
FT                   /organism="Pseudomonas aeruginosa"
FT                   /strain="PAC"
FT                   /isolate="PAC 1"
FT                   /map="38 min"
FT   CDS             1289..1879
FT                   /db_xref="SWISS-PROT:P10932"
FT                   /note="aliphatic amidase regulator, positive  regulator of
FT                   amiE"
FT                   /transl_table=11
FT                   /gene="amiR"
FT                   /protein_id="CAA32023.1"
FT                   /translation="MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWP
P
FT                   PEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECH
G
FT                   VITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGW
D
FT                   EREAHQHLSREAMKRREPILKIAQELLGNEPSA"
FT   CDS             135..1292
FT                   /db_xref="SWISS-PROT:P27017"
FT                   /note="negative regulator of amiR"
FT                   /transl_table=11
FT                   /gene="amiC"
FT                   /protein_id="CAA32024.1"
FT                   /translation="MGSHQERPLIGLLFSETGVTADIERSHAYGALLAVEQLNREGGV
G
FT                   GRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLC
Y
FT                   PTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRH
L
FT                   YRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRY
G
FT                   DGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTPASRAFVQACHGFFPENA
T
FT                   ITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLS
S
FT                   RIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP"
FT   promoter        8..24
FT                   /note="proposed rpoN-dependent promoter"
FT   promoter        65..81
FT                   /note="proposed rpoN-dependent promoter"
FT   RBS             121..126
FT                   /note="proposed Shine-Dalgarno sequence"
FT   mutation        912..1167
FT                   /note="ClaI fragment deleted in pSW36,  constitutive
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]

Output file format

   The output is a text representation of the feature table, and goes by
   default to standard output (the terminal).
   
   Here is the output from the example run:

PAAMIR
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
|==========================================================| 2167
|----------------------------------------------------------> source
>                                                            promoter
|>                                                           promoter
  >                                                          RBS
  |------------------------------->                          CDS
                |>                                           misc_feature
                        |------>                             mutation
                                  |---------------->         CDS
|                                                            misc_feature
                                  |                          conflict

Data files

   None.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with a status of 0.
   
Known bugs

   None.
   
See also

   Program name Description
   abiview Reads ABI file and display the trace
   cirdna Draws circular maps of DNA constructs
   coderet Extract CDS, mRNA and translations from feature tables
   extractfeat Extract features from a sequence
   lindna Draws linear maps of DNA constructs
   maskfeat Mask off features of a sequence
   pepnet Displays proteins as a helical net
   pepwheel Shows protein sequences as helices
   prettyplot Displays aligned sequences, with colouring and boxing
   prettyseq Output sequence with translated ranges
   remap Display a sequence with restriction cut sites, translation etc
   seealso Finds programs sharing group names
   showalign Displays a multiple sequence alignment
   showdb Displays information on the currently available databases
   showseq Display a sequence with features, translation etc
   swissparse Retrieves sequences from swissprot using keyword search
   textsearch Search sequence documentation text. SRS and Entrez are
   faster!
   
Author(s)

   This application was written by Gary Williams
   (gwilliam@hgmp.mrc.ac.uk)
   
History

   Written 1999 - Gary Williams
   
   Dec 2001 - added -sort nosort option to get the features in the input
   order
   
Target users

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