EMBOSS: showfeat

| showfeat

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## Function

Display features of a sequence in pretty format

## Description

showfeat reads one or more protein or nucleic sequences with associated feature tables, and writes the features to file (or screen) in a style suitable for publication. There are many options for controlling the format of the output.

## Usage

Here is a sample session with showfeat

    % showfeat
    Display features of a sequence in pretty format
    Input sequence(s): tembl:x65921
    Output file [x65921.showfeat]:

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

Example 2

Display 'joined' features on one line with positions:

    % showfeat -joinfeat -pos
    Display features of a sequence in pretty format
    Input sequence(s): tembl:x65921
    Output file [x65921.showfeat]:

Go to the output files for this example

Example 3

Display just positions and names of CDS features - this can be used as a regions file in showseq:

    % showfeat -typematch CDS -width 0 -noid -nodesc -noscale -pos
    Display features of a sequence in pretty format
    Input sequence(s): tembl:x65921
    Output file [x65921.showfeat]:

Go to the output files for this example

## Command line arguments

    Display features of a sequence in pretty format
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-sequence]          seqall     Sequence(s) filename and optional format, or
                                      reference (input USA)
      [-outfile]           outfile    [*.showfeat] Output file name

       Additional (Optional) qualifiers:
       -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)
       -tagmatch           string     [*] Tags are the types of extra values that
                                      a feature may have. For example in the EMBL
                                      feature table, a 'CDS' type of feature may
                                      have the tags '/codon', '/codon_start',
                                      '/db_xref', '/EC_number', '/evidence',
                                      '/exception', '/function', '/gene',
                                      '/label', '/map', '/note', '/number',
                                      '/partial', '/product', '/protein_id',
                                      '/pseudo', '/standard_name', '/translation',
                                      '/transl_except', '/transl_table', or
                                      '/usedin'. Some of these tags also have
                                      values, for example '/gene' can have the
                                      value of the gene name.
                                      By default any feature tag in the feature
                                      table is shown. You can set this to match
                                      any feature tag you wish to show.
                                      The tag may be wildcarded by using '*'.
                                      If you wish to show more than one tag,
                                      separate their names with the character '|',
                                      eg:
                                      gene | label (Any string)
       -valuematch         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 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)
       -sort               menu       [start] Sort features by Type, Start or
                                      Source, Nosort (don't sort - use input
                                      order) or join coding regions together and
                                      leave other features in the input order
                                      (Values: source (Sort by Source); start
                                      (Sort by Start position); type (Sort by
                                      Type); nosort (No sorting done))
       -joinfeatures       boolean    [N] Join coding regions together
       -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'.

       Advanced (Unprompted) qualifiers:
       -html               boolean    [N] Use HTML formatting
       -[no]id             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.
       -[no]scale          boolean    [Y] Set this to be false if you do not wish
                                      to display the scale line.
       -width              integer    [60] 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)
       -collapse           boolean    [N] 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        boolean    [Y] Set this to be false if you do not wish
                                      to display forward sense features.
       -[no]reverse        boolean    [Y] Set this to be false if you do not wish
                                      to display reverse sense features.
       -[no]unknown        boolean    [Y] 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             boolean    [N] 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
                                      '-'.
       -sourceshow         boolean    [N] Set this if you wish to display the
                                      origin 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           boolean    [N] 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]typeshow       boolean    [Y] Set this to be false if you do not wish
                                      to display the type of the features.
       -tagshow            boolean    [N] Set this to be false if you do not wish
                                      to display the tags and values of the
                                      features.
       -[no]valueshow      boolean    [Y] 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.
       -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.

       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
       -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

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1) | seqall | Sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
[-outfile] (Parameter 2) | outfile | Output file name | Output file | <*>.showfeat
Additional (Optional) qualifiers
-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 | *
-tagmatch | string | Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Some of these tags also have values, for example '/gene' can have the value of the gene name. By default any feature tag in the feature table is shown. You can set this to match any feature tag you wish to show. The tag may be wildcarded by using '*'. If you wish to show more than one tag, separate their names with the character '|', eg: gene | label | Any string | *
-valuematch | 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 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 | *
-sort | list | Sort features by Type, Start or Source, Nosort (don't sort - use input order) or join coding regions together and leave other features in the input order |
source | (Sort by Source)
start | (Sort by Start position)
type | (Sort by Type)
nosort | (No sorting done)
| start
-joinfeatures | boolean | Join coding regions together | Boolean value Yes/No | No
-annotation | range | Regions to annotate by marking. If this is left blank, then no annotation is added. A set of regions is specified by a set of pairs of positions followed by optional text. The positions are integers. They are followed by any text (but not digits when on the command-line). Examples of region specifications are: 24-45 new domain 56-78 match to Mouse 1-100 First part 120-156 oligo A file of ranges to annotate (one range per line) can be specified as '@filename'. | Sequence range | If this is left blank, then no annotation is added.
Advanced (Unprompted) qualifiers
-html | boolean | Use HTML formatting | Boolean value Yes/No | No
-[no]id | boolean | Set this to be false if you do not wish to display the ID name of the sequence. | Boolean value Yes/No | Yes
-[no]description | boolean | Set this to be false if you do not wish to display the description of the sequence. | Boolean value Yes/No | Yes
-[no]scale | boolean | Set this to be false if you do not wish to display the scale line. | Boolean value Yes/No | Yes
-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. | Integer 0 or more | 60
-collapse | boolean | 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. | Boolean value Yes/No | No
-[no]forward | boolean | Set this to be false if you do not wish to display forward sense features. | Boolean value Yes/No | Yes
-[no]reverse | boolean | Set this to be false if you do not wish to display reverse sense features. | Boolean value Yes/No | Yes
-[no]unknown | boolean | 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)). | Boolean value Yes/No | Yes
-strand | boolean | 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 '-'. | Boolean value Yes/No | No
-sourceshow | boolean | Set this if you wish to display the origin 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. | Boolean value Yes/No | No
-position | boolean | 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'. | Boolean value Yes/No | No
-[no]typeshow | boolean | Set this to be false if you do not wish to display the type of the features. | Boolean value Yes/No | Yes
-tagshow | boolean | Set this to be false if you do not wish to display the tags and values of the features. | Boolean value Yes/No | No
-[no]valueshow | boolean | 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. | Boolean value Yes/No | Yes
-stricttags | boolean | By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed. If this is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed. | Boolean value Yes/No | No
Associated qualifiers
"-sequence" associated seqall qualifiers
-sbegin1 -sbegin_sequence | integer | Start of each sequence to be used | Any integer value | 0
-send1 -send_sequence | integer | End of each sequence to be used | Any integer value | 0
-sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N
-sformat1 -sformat_sequence | string | Input sequence format | Any string |
-iquery1 -iquery_sequence | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_sequence | string | Database name | Any string |
-sid1 -sid_sequence | string | Entryname | Any string |
-ufo1 -ufo_sequence | string | UFO features | Any string |
-fformat1 -fformat_sequence | string | Features format | Any string |
-fopenfile1 -fopenfile_sequence | string | Features file name | Any string |
"-outfile" associated outfile qualifiers
-odirectory2 -odirectory_outfile | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## Input file format

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

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

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

The input format can be specified by using the command-line qualifier `-sformat xxx`, where 'xxx' is replaced by the name of the required format. The available format names are: text, html, xml (uniprotxml), obo, embl (swissprot)

Where the sequence format has no feature information, a second file can be read to load the feature data. The file is specified with the qualifier `-ufo xxx` and the feature format is specified with the qualifier `-fformat xxx`

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

See: http://emboss.sf.net/docs/themes/FeatureFormats.html for further information on feature formats.

### Input files for usage example

'tembl:x65921' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:x65921

    ID   X65921; SV 1; linear; genomic DNA; STD; HUM; 2016 BP.
    XX
    AC   X65921; S45242;
    XX
    DT   13-MAY-1992 (Rel. 31, Created)
    DT   14-NOV-2006 (Rel. 89, Last updated, Version 7)
    XX
    DE   H.sapiens fau 1 gene
    XX
    KW   fau 1 gene.
    XX
    OS   Homo sapiens (human)
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
    OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
    OC   Homo.
    XX
    RN   [1]
    RP   1-2016
    RA   Kas K.;
    RT   ;
    RL   Submitted (29-APR-1992) to the INSDC.
    RL   K. Kas, University of Antwerp, Dept of Biochemistry T3.22,
    RL   Universiteitsplein 1, 2610 Wilrijk, BELGIUM
    XX
    RN   [2]
    RP   1-2016
    RX   DOI; 10.1016/0006-291X(92)91286-Y.
    RX   PUBMED; 1326960.
    RA   Kas K., Michiels L., Merregaert J.;
    RT   "Genomic structure and expression of the human fau gene: encoding the
    RT   ribosomal protein S30 fused to a ubiquitin-like protein";
    RL   Biochem. Biophys. Res. Commun. 187(2):927-933(1992).
    XX
    DR   Ensembl-Gn; ENSG00000149806; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000279259; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000434372; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000525297; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000526555; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000527548; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000529259; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000529639; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000531743; Homo_sapiens.
    DR   GDB; 191789.
    DR   GDB; 191790.
    DR   GDB; 354872.
    DR   GDB; 4590236.
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   source          1..2016

      [Part of this file has been deleted for brevity]

    FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
    FT   intron          857..950
    FT                   /number=2
    FT   exon            951..1095
    FT                   /number=3
    FT   intron          1096..1556
    FT                   /number=3
    FT   exon            1557..1612
    FT                   /number=4
    FT   intron          1613..1786
    FT                   /number=4
    FT   exon            1787..>1912
    FT                   /number=5
    FT   polyA_signal    1938..1943
    XX
    SQ   Sequence 2016 BP; 421 A; 562 C; 538 G; 495 T; 0 other;
         ctaccatttt ccctctcgat tctatatgta cactcgggac aagttctcct gatcgaaaac        60
         ggcaaaacta aggccccaag taggaatgcc ttagttttcg gggttaacaa tgattaacac       120
         tgagcctcac acccacgcga tgccctcagc tcctcgctca gcgctctcac caacagccgt       180
         agcccgcagc cccgctggac accggttctc catccccgca gcgtagcccg gaacatggta       240
         gctgccatct ttacctgcta cgccagcctt ctgtgcgcgc aactgtctgg tcccgccccg       300
         tcctgcgcga gctgctgccc aggcaggttc gccggtgcga gcgtaaaggg gcggagctag       360
         gactgccttg ggcggtacaa atagcaggga accgcgcggt cgctcagcag tgacgtgaca       420
         cgcagcccac ggtctgtact gacgcgccct cgcttcttcc tctttctcga ctccatcttc       480
         gcggtagctg ggaccgccgt tcaggtaaga atggggcctt ggctggatcc gaagggcttg       540
         tagcaggttg gctgcggggt cagaaggcgc ggggggaacc gaagaacggg gcctgctccg       600
         tggccctgct ccagtcccta tccgaactcc ttgggaggca ctggccttcc gcacgtgagc       660
         cgccgcgacc accatcccgt cgcgatcgtt tctggaccgc tttccactcc caaatctcct       720
         ttatcccaga gcatttcttg gcttctctta caagccgtct tttctttact cagtcgccaa       780
         tatgcagctc tttgtccgcg cccaggagct acacaccttc gaggtgaccg gccaggaaac       840
         ggtcgcccag atcaaggtaa ggctgcttgg tgcgccctgg gttccatttt cttgtgctct       900
         tcactctcgc ggcccgaggg aacgcttacg agccttatct ttccctgtag gctcatgtag       960
         cctcactgga gggcattgcc ccggaagatc aagtcgtgct cctggcaggc gcgcccctgg      1020
         aggatgaggc cactctgggc cagtgcgggg tggaggccct gactaccctg gaagtagcag      1080
         gccgcatgct tggaggtgag tgagagagga atgttctttg aagtaccggt aagcgtctag      1140
         tgagtgtggg gtgcatagtc ctgacagctg agtgtcacac ctatggtaat agagtacttc      1200
         tcactgtctt cagttcagag tgattcttcc tgtttacatc cctcatgttg aacacagacg      1260
         tccatgggag actgagccag agtgtagttg tatttcagtc acatcacgag atcctagtct      1320
         ggttatcagc ttccacacta aaaattaggt cagaccaggc cccaaagtgc tctataaatt      1380
         agaagctgga agatcctgaa atgaaactta agatttcaag gtcaaatatc tgcaactttg      1440
         ttctcattac ctattgggcg cagcttctct ttaaaggctt gaattgagaa aagaggggtt      1500
         ctgctgggtg gcaccttctt gctcttacct gctggtgcct tcctttccca ctacaggtaa      1560
         agtccatggt tccctggccc gtgctggaaa agtgagaggt cagactccta aggtgagtga      1620
         gagtattagt ggtcatggtg ttaggacttt ttttcctttc acagctaaac caagtccctg      1680
         ggctcttact cggtttgcct tctccctccc tggagatgag cctgagggaa gggatgctag      1740
         gtgtggaaga caggaaccag ggcctgatta accttccctt ctccaggtgg ccaaacagga      1800
         gaagaagaag aagaagacag gtcgggctaa gcggcggatg cagtacaacc ggcgctttgt      1860
         caacgttgtg cccacctttg gcaagaagaa gggccccaat gccaactctt aagtcttttg      1920
         taattctggc tttctctaat aaaaaagcca cttagttcag tcatcgcatt gtttcatctt      1980
         tacttgcaag gcctcaggga gaggtgtgct tctcgg                                2016
    //

## Output file format

The output is a text representation of the feature table.

### Output files for usage example

### File: x65921.showfeat

    X65921
    H.sapiens fau 1 gene
    |==========================================================| 2016
    |----------------------------------------------------------> source
               |-->                                              exon
               |-->                                              mRNA
                          |->                                    mRNA
                               |--->                             mRNA
                                                 |>              mRNA
                                                        |-->     mRNA
                  |------->                                      intron
                          |->                                    exon
                          |->                                    CDS
                               |--->                             CDS
                                                 |>              CDS
                                                        |-->     CDS
                            |-->                                 intron
                               |--->                             exon
                                   |------------->               intron
                                                 |>              exon
                                                   |---->        intron
                                                        |-->     exon
                                                            >    polyA_signal

### Output files for usage example 2

### File: x65921.showfeat

    X65921
    H.sapiens fau 1 gene
    |==========================================================| 2016
    |----------------------------------------------------------> 1-2016 source
               |-->                                              408-504 exon
               |-->       |->  |--->             |>     |-->     408-504,774-856,951-1095,1557-1612,1787-1912 mRNA
                  |------->                                      505-773 intron
                          |->                                    774-856 exon
                          |->  |--->             |>     |-->     782-856,951-1095,1557-1612,1787-1912 CDS
                            |-->                                 857-950 intron
                               |--->                             951-1095 exon
                                   |------------->               1096-1556 intron
                                                 |>              1557-1612 exon
                                                   |---->        1613-1786 intron
                                                        |-->     1787-1912 exon
                                                            >    1938-1943 polyA_signal

### Output files for usage example 3

### File: x65921.showfeat

    782-856 CDS
    951-1095 CDS
    1557-1612 CDS
    1787-1912 CDS

## Data files

None.

## Notes

Sequence regions to annotate may be specified as a set or ranges. Optionally, forward and reverse sense features, and features of unspecified sense (for example, CG-rich regions), are displayed. Optionally, features from the same source and of the same type and sense may all be printed on the same line, although this may make it hard to distinguish overlapping features.

By default, any features in the feature table are displayed however there are options to restrict this by feature source, type, feature tag and feature tag value.

Features may be sorted by Type, Start or Source, left unsorted (in which case the same order as the input is used), or features for the coding regions presented all together.

Various options control what else is displayed, including the sequence ID, description, scale line, width of display, strand of the features, feature source, start and end positions, feature type, and feature tags and tag values. 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.

Optionally, output can be in HTML.

## 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 | Display the trace in an ABI sequencer file
cirdna | Draw circular map of DNA constructs
extractfeat | Extract features from sequence(s)
iep | Calculate the isoelectric point of proteins
lindna | Draw linear maps of DNA constructs
maskfeat | Write a sequence with masked features
pepinfo | Plot amino acid properties of a protein sequence in parallel
pepnet | Draw a helical net for a protein sequence
pepwheel | Draw a helical wheel diagram for a protein sequence
plotorf | Plot potential open reading frames in a nucleotide sequence
prettyplot | Draw a sequence alignment with pretty formatting
prettyseq | Write a nucleotide sequence and its translation to file
remap | Display restriction enzyme binding sites in a nucleotide sequence
showpep | Display protein sequences with features in pretty format
sixpack | Display a DNA sequence with 6-frame translation and ORFs
twofeat | Find neighbouring pairs of features in sequence(s)

## Author(s)

Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## 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

None