Inputsection-sequenceseqallAdditionalsection-sourcematchstring
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 Default value: *
-typematchstring
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 Default value: *
-tagmatchstring
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 Default value: *
-valuematchstring
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 Default value: *
-sortlist
Default value: start
-joinfeaturesboolean
Default value: N
-annotationrange
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'.
Advancedsection-htmlboolean
Default value: N
-idboolean
Set this to be false if you do not wish to display the ID name of the sequence. Default value: Y
-descriptionboolean
Set this to be false if you do not wish to display the description of the sequence. Default value: Y
-scaleboolean
Set this to be false if you do not wish to display the scale line. Default value: Y
-widthinteger
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. Default value: 60
-collapseboolean
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.
Default value: N
-forwardboolean
Set this to be false if you do not wish to display forward sense features. Default value: Y
-reverseboolean
Set this to be false if you do not wish to display reverse sense features. Default value: Y
-unknownboolean
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)). Default value: Y
-strandboolean
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 '-'. Default value: N
-originboolean
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. Default value: N
-positionboolean
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'. Default value: N
-typeboolean
Set this to be false if you do not wish to display the type of the features. Default value: Y
-tagsboolean
Set this to be false if you do not wish to display the tags and values of the features. Default
value: N
-valuesboolean
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. Default value: Y
-stricttagsboolean
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. Default value:
N
Outputsection-outfileoutfile
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