Tehdyt toimenpiteet
|
showfeat |
Wiki
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Function
Display features of a sequence in pretty formatDescription
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:6.4.0.0
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
'-'.
-origin 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]type boolean [Y] Set this to be false if you do not wish
to display the type of the features.
-tags boolean [N] Set this to be false if you do not wish
to display the tags and values of the
features.
-[no]values 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
-sformat1 string Input sequence format
-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 |
|
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 | ||||||||
| -origin | 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]type | boolean | Set this to be false if you do not wish to display the type of the features. | Boolean value Yes/No | Yes | ||||||||
| -tags | 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]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. | 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 | ||||||||
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |||||||||
| -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 EMBL/GenBank/DDBJ databases.
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 GDB; 191789.
DR GDB; 191790.
DR GDB; 354872.
DR GDB; 4590236.
XX
FH Key Location/Qualifiers
FH
FT source 1..2016
FT /organism="Homo sapiens"
FT /mol_type="genomic DNA"
FT /clone_lib="CML cosmid"
FT /clone="15.1"
FT /db_xref="taxon:9606"
FT mRNA join(408..504,774..856,951..1095,1557..1612,1787..>1912)
FT /gene="fau 1"
FT exon 408..504
FT /number=1
[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 | Draws circular maps of DNA constructs |
| extractfeat | Extract features from sequence(s) |
| iep | Calculate the isoelectric point of proteins |
| lindna | Draws 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 | Displays protein sequences with features in pretty format |
| sixpack | Display a DNA sequence with 6-frame translation and ORFs |
| twofeat | Finds 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 WilliamsDec 2001 - added -sort nosort option to get the features in the input order