Provided by: emboss_6.6.0+dfsg-12ubuntu1_amd64 
NAME
showseq - Displays sequences with features in pretty format
SYNOPSIS
showseq -sequence seqall -mfile datafile -format list -things list [-translate range]
[-revtranslate range] [-uppercase range] [-highlight range] [-annotation range]
[-enzymes string] [-table list] [-sourcematch string] [-typematch string]
[-sensematch integer] [-minscore float] [-maxscore float] [-tagmatch string]
[-valuematch string] [-stricttags boolean] -flatreformat boolean -mincuts integer
-maxcuts integer -sitelen integer -single boolean -blunt boolean -sticky boolean
-ambiguity boolean -plasmid boolean -methylation boolean -commercial boolean
-limit boolean -orfminsize integer -threeletter boolean -number boolean
-width integer -length integer -margin integer -name boolean -description boolean
-offset integer -html boolean -outfile outfile
showseq -help
DESCRIPTION
showseq is a command line program from EMBOSS (“the European Molecular Biology Open
Software Suite”). It is part of the "Nucleic:Translation,Nucleic:Restriction" command
group(s).
OPTIONS
Input section
-sequence seqall
-mfile datafile
Default value: Emethylsites.dat
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, complement sequence, ticks line, frame 1
translation, blank line; then you should enter 'S,C,T,1,B'. Default value: B,N,T,S,A,F
Additional section
-translate range
Regions to translate (if translating). If this is left blank the complete sequence is
translated. 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
-revtranslate range
Regions to translate (if translating). If this is left blank the complete sequence is
translated. 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: 78-56, 45-24, 888..765, 99=67; 45:1
-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'.
-enzymes string
The name 'all' reads in all enzyme names from the REBASE database. You can specify
enzymes by giving their names with commas between then, such as:
'HincII,hinfI,ppiI,hindiii'. The case of the names is not important. You can specify a
file of enzyme names to read in by giving the name of the file holding the enzyme
names with a '@' character in front of it, for example, '@enz.list'. Blank lines and
lines starting with a hash character or '!' are ignored and all other lines are
concatenated together with a comma character ',' and then treated as the list of
enzymes to search for. An example of a file of enzyme names is: ! my enzymes HincII,
ppiII ! other enzymes hindiii HinfI PpiI Default value: all
-table list
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: *
-sensematch integer
By default any feature type in the feature table is shown. You can set this to match
any feature sense you wish to show. 0 - any sense, 1 - forward sense, -1 - reverse
sense
-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. 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: *
-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
Restriction map options
-flatreformat boolean
This changes the output format to one where the recognition site is indicated by a row
of '===' characters and the cut site is pointed to by a '>' character in the forward
sense, or a '<' in the reverse sense strand. Default value: N
-mincuts integer
This sets the minimum number of cuts for any restriction enzyme that will be
considered. Any enzymes that cut fewer times than this will be ignored. Default value:
1
-maxcuts integer
This sets the maximum number of cuts for any restriction enzyme that will be
considered. Any enzymes that cut more times than this will be ignored. Default value:
2000000000
-sitelen integer
This sets the minimum length of the restriction enzyme recognition site. Any enzymes
with sites shorter than this will be ignored. Default value: 4
-single boolean
If this is set then this forces the values of the mincuts and maxcuts qualifiers to
both be 1. Any other value you may have set them to will be ignored. Default value: N
-blunt boolean
This allows those enzymes which cut at the same position on the forward and reverse
strands to be considered. Default value: Y
-sticky boolean
This allows those enzymes which cut at different positions on the forward and reverse
strands, leaving an overhang, to be considered. Default value: Y
-ambiguity boolean
This allows those enzymes which have one or more 'N' ambiguity codes in their pattern
to be considered Default value: Y
-plasmid boolean
If this is set then this allows searches for restriction enzyme recognition site and
cut positions that span the end of the sequence to be considered. Default value: N
-methylation boolean
If this is set then RE recognition sites will not match methylated bases. Default
value: N
-commercial boolean
If this is set, then only those enzymes with a commercial supplier will be searched
for. This qualifier is ignored if you have specified an explicit list of enzymes to
search for, rather than searching through 'all' the enzymes in the REBASE database. It
is assumed that, if you are asking for an explicit enzyme, then you probably know
where to get it from and so all enzymes names that you have asked to be searched for,
and which cut, will be reported whether or not they have a commercial supplier.
Default value: Y
-limit boolean
This limits the reporting of enzymes to just one enzyme from each group of
isoschizomers. The enzyme chosen to represent an isoschizomer group is the prototype
indicated in the data file 'embossre.equ', which is created by the program
'rebaseextract'. If you prefer different prototypes to be used, make a copy of
embossre.equ in your home directory and edit it. If this value is set to be false then
all of the input enzymes will be reported. You might like to set this to false if you
are supplying an explicit set of enzymes rather than searching 'all' of them. Default
value: Y
-orfminsize integer
This sets the minimum size of Open Reading Frames (ORFs) to display in the
translations. All other translation regions are masked by changing the amino acids to
'-' characters.
-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
showseq 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.