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

BUGS

       Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or
       directly to the EMBOSS developers
       (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

       showpep is fully documented via the tfm(1) system.

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
           Wrote the script used to autogenerate this manual page.

COPYRIGHT

       This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package.
       It can be redistributed under the same terms as EMBOSS itself.