SHOWSEQ(1e) | EMBOSS Manual for Debian | SHOWSEQ(1e) |
NAME¶
showseq - Displays sequences with features in pretty formatSYNOPSIS¶
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 datafileDefault value: Emethylsites.dat
Required section¶
-format listDefault 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 rangeRegions 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 stringBy 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 booleanThis 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 outfileBUGS¶
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.05/11/2012 | EMBOSS 6.4.0 |