Additional section¶
-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 Default
value: *
-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
Default value: *
-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 Default value: *
-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 Default value: *
-sort list
Default value: start
-joinfeatures boolean
Default value: N
-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'.
Advanced section¶
-html boolean
Default value: N
-id boolean
Set this to be false if you do not wish to display the ID
name of the sequence. Default value: Y
-description boolean
Set this to be false if you do not wish to display the
description of the sequence. Default value: Y
-scale boolean
Set this to be false if you do not wish to display the
scale line. Default value: Y
-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.
Default value: 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. Default
value: N
-forward boolean
Set this to be false if you do not wish to display
forward sense features. Default value: Y
-reverse boolean
Set this to be false if you do not wish to display
reverse sense features. Default value: Y
-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)). Default value: Y
-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 '-'. Default value: N
-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. Default value: N
-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'. Default value: N
-type boolean
Set this to be false if you do not wish to display the
type of the features. Default value: Y
-tags boolean
Set this to be false if you do not wish to display the
tags and values of the features. Default value: N
-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. Default value: Y
-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. Default
value: N
