showpepe - Online in the Cloud

PROGRAM:

NAME

showpep - Displays protein sequences with features in pretty format

SYNOPSIS

showpep -sequence seqall -format list -things list [-uppercase range] [-highlight range]
[-annotation range] [-sourcematch string] [-typematch string] [-minscore float]
[-maxscore float] [-tagmatch string] [-valuematch string] [-stricttags boolean]
-threeletter boolean -number boolean -width integer -length integer
-margin integer -name boolean -description boolean -offset integer -html boolean
-outfile outfile

showpep -help

DESCRIPTION

showpep is a command line program from EMBOSS (“the European Molecular Biology Open
Software Suite”). It is part of the "Display" command group(s).

OPTIONS

Input section
-sequence seqall

Required section
-format list
Default value: 2

-things list
Specify a list of one or more code characters in the order in which you wish things to
be displayed one above the other down the page. For example if you wish to see things
displayed in the order: sequence, ticks line, blank line; then you should enter
'S,T,B'. Default value: B,N,T,S,A,F

Additional section
-uppercase range
Regions to put in uppercase. If this is left blank, then the sequence case is left
alone. A set of regions is specified by a set of pairs of positions. The positions are
integers. They are separated by any non-digit, non-alpha character. Examples of region
specifications are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99

-highlight range
Regions to colour if formatting for HTML. If this is left blank, then the sequence is
left alone. A set of regions is specified by a set of pairs of positions. The
positions are integers. They are followed by any valid HTML font colour. Examples of
region specifications are: 24-45 blue 56-78 orange 1-100 green 120-156 red A file of
ranges to colour (one range per line) can be specified as '@filename'.

-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'.

Feature display options
-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: *

-minscore float
Minimum score of feature to display (see also maxscore) Default value: 0.0

-maxscore float
Maximum score of feature to display. If both minscore and maxscore are zero (the
default), then any score is ignored Default value: 0.0

-tagmatch string
Tags are the types of extra values that a feature may have. 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. 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: *

-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

Advanced section
-threeletter boolean
Default value: N

-number boolean
Default value: N

-width integer
Default value: 60

-length integer

-margin integer
Default value: 10

-name 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

-offset integer
Default value: 1

-html boolean
Default value: N

Output section
-outfile outfile

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