| SHOWSEQ(1e) | EMBOSS Manual for Debian | SHOWSEQ(1e) |
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.
| 05/11/2012 | EMBOSS 6.4.0 |