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 em:paamir
Show features of a sequence.
Output file [paamir.showfeat]: stdout
PAAMIR
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
|==========================================================| 2167
>                                                            misc_feature
|----------------------------------------------------------> source
>                                                            promoter
|>                                                           promoter
  >                                                          RBS
  |------------------------------->                          CDS
                |>                                           misc_feature
                        |------>                             variation
                                  >                          conflict
                                  |---------------->         CDS



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,
                                  Nosort (don't sort - use input order) or
                                  join coding regions together and leave other
                                  features in the input order

   Advanced qualifiers:
   -html               boolean    Use HTML formatting
   -[no]id             boolean    Set this to be false if you do not wish to
                                  display the ID name of the sequence.
   -[no]description    boolean    Set this to be false if you do not wish to
                                  display the description of the sequence.
   -[no]scale          boolean    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           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.
   -[no]forward        boolean    Set this to be false if you do not wish to
                                  display forward sense features.
   -[no]reverse        boolean    Set this to be false if you do not wish to
                                  display reverse sense features.
   -[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)).
   -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 '-'.
   -source             boolean    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           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'.
   -[no]type           boolean    Set this to be false if you do not wish to
                                  display the type of the features.
   -tags               boolean    Set this to be false if you do not wish to
                                  display the tags and values of the features.
   -[no]values         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.

   General qualifiers:
  -help                boolean    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 <sequence>.showfeat
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, 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)
join (Join coding regions together)
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.

Here is the output from the example run:


|==========================================================| 2167
>                                                            misc_feature
|----------------------------------------------------------> source
>                                                            promoter
|>                                                           promoter
  >                                                          RBS
  |------------------------------->                          CDS
                |>                                           misc_feature
                        |------>                             variation
                                  >                          conflict
                                  |---------------->         CDS


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 nameDescription
abiviewReads ABI file and display the trace
cirdnaDraws circular maps of DNA constructs
coderetExtract CDS, mRNA and translations from feature tables
extractfeatExtract features from a sequence
lindnaDraws linear maps of DNA constructs
maskfeatMask off features of a sequence
pepnetDisplays proteins as a helical net
pepwheelShows protein sequences as helices
prettyplotDisplays aligned sequences, with colouring and boxing
prettyseqOutput sequence with translated ranges
remapDisplay a sequence with restriction cut sites, translation etc
seealsoFinds programs sharing group names
showalignDisplays a multiple sequence alignment
showdbDisplays information on the currently available databases
showseqDisplay a sequence with features, translation etc
swissparseRetrieves sequences from swissprot using keyword search
textsearchSearch 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