EMBOSS: showfeat

| ## 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="MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPP
    FT                   PEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHG
    FT                   VITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWD
    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="MGSHQERPLIGLLFSETGVTADIERSHAYGALLAVEQLNREGGVG
    FT                   GRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCY
    FT                   PTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHL
    FT                   YRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYG
    FT                   DGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTPASRAFVQACHGFFPENAT
    FT                   ITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSS
    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 causes
    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