Tehdyt toimenpiteet
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showseq |
Wiki
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Function
Displays sequences with features in pretty formatDescription
showseq displays one or more nucleic acid sequences, with features, in a style suitable for publication. The output is sent to screen by default but can be written to file. You may pick a format from a list, alternatively, use the many options to control what is output and in what format. Optionally, the sequence feature table can be displayed. The sequence can be translated, using the specified genetic code tables. Also recognition sites and/or cut sites of restriction enzymes from the REBASE database may be displayed. There are various other options for controlling how the sequence is displayed and numbered and the output can be formatted for HTML.
Usage
Here is a sample session with showseq
% showseq tembl:x13776 -sbeg 1 -send 100
Displays sequences with features in pretty format
Things to display
0 : Enter your own list of things to display
1 : Sequence only
2 : Default sequence with features
3 : Pretty sequence
4 : One frame translation
5 : Three frame translations
6 : Six frame translations
7 : Restriction enzyme map
8 : Baroque
Display format [2]:
Output file [x13776.showseq]:
|
Go to the input files for this example
Go to the output files for this example
Example 2
The standard list of output formats are only a small selection of the possible ways in which a sequence might be displayed. Precise control over the output format is acheived by selecting the qualifier '-format 0' (Option 0 in the list of things to display). For example, by choosing format '0' and then specifying that we want to display the things: 'b,s,t,c', we will output the sequence in the following way:
% showseq tembl:x13776 -sbeg 1 -send 120
Displays sequences with features in pretty format
Things to display
0 : Enter your own list of things to display
1 : Sequence only
2 : Default sequence with features
3 : Pretty sequence
4 : One frame translation
5 : Three frame translations
6 : Six frame translations
7 : Restriction enzyme map
8 : Baroque
Display format [2]: 0
Specify your own things to display
S : Sequence
B : Blank line
1 : Frame1 translation
2 : Frame2 translation
3 : Frame3 translation
-1 : CompFrame1 translation
-2 : CompFrame2 translation
-3 : CompFrame3 translation
T : Ticks line
N : Number ticks line
C : Complement sequence
F : Features
R : Restriction enzyme cut sites in forward sense
-R : Restriction enzyme cut sites in reverse sense
A : Annotation
Enter a list of things to display [B,N,T,S,A,F]: b,s,t,c
Output file [x13776.showseq]:
|
Go to the output files for this example
Example 3
Display only the sequence:
% showseq tembl:x13776 -sbeg 1 -send 100 -noname -nodesc -format 0 -thing S Displays sequences with features in pretty format Output file [x13776.showseq]: |
Go to the output files for this example
Example 4
Number the sequence lines in the margin:
% showseq tembl:x13776 -sbeg 1 -send 100 -format 1 -number Displays sequences with features in pretty format Output file [x13776.showseq]: |
Go to the output files for this example
Example 5
Start the numbering at a specified value ('123' in this case):
% showseq tembl:x13776 -sbeg 1 -send 100 -format 1 -number -offset 123 Displays sequences with features in pretty format Output file [x13776.showseq]: |
Go to the output files for this example
Example 6
Make selected regions uppercase. (Use '-slower' to force the rest of the sequence to be lowercase).
% showseq tembl:x13776 -sbeg 1 -send 100 -format 1 -slower -upper "8-24,65-81" Displays sequences with features in pretty format Output file [x13776.showseq]: |
Go to the output files for this example
Example 7
Translate selected regions:
% showseq tembl:x13776 -sbeg 1 -send 120 -format 5 -trans 25-49,66-76 Displays sequences with features in pretty format Output file [x13776.showseq]: |
Go to the output files for this example
Example 8
Add your own annotation to the display:
% showseq tembl:x13776 -sbeg 1 -send 100 -format 2 -send 120 -annotation "13-26 binding site 15-15 SNP" Displays sequences with features in pretty format Output file [x13776.showseq]: |
Go to the output files for this example
Command line arguments
Displays sequences with features in pretty format
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers (* if not always prompted):
[-sequence] seqall (Gapped) nucleotide sequence(s) filename and
optional format, or reference (input USA)
-format menu [2] Display format (Values: 0 (Enter your
own list of things to display); 1 (Sequence
only); 2 (Default sequence with features); 3
(Pretty sequence); 4 (One frame
translation); 5 (Three frame translations);
6 (Six frame translations); 7 (Restriction
enzyme map); 8 (Baroque))
* -things menu [B,N,T,S,A,F] 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'. (Values: S
(Sequence); B (Blank line); 1 (Frame1
translation); 2 (Frame2 translation); 3
(Frame3 translation); -1 (CompFrame1
translation); -2 (CompFrame2 translation);
-3 (CompFrame3 translation); T (Ticks line);
N (Number ticks line); C (Complement
sequence); F (Features); R (Restriction
enzyme cut sites in forward sense); -R
(Restriction enzyme cut sites in reverse
sense); A (Annotation))
[-outfile] outfile [*.showseq] Output file name
Additional (Optional) qualifiers:
-translate range [If this is left blank the complete sequence
is translated.] 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 [If this is left blank the complete reverse
sequence is translated.] 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 [If this is left blank, then the sequence
case is left alone.] 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 [(full sequence)] 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 [If this is left blank, then no annotation
is added.] 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 [all] 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 (Any string)
-table menu [0] Genetic code to use (Values: 0
(Standard); 1 (Standard (with alternative
initiation codons)); 2 (Vertebrate
Mitochondrial); 3 (Yeast Mitochondrial); 4
(Mold, Protozoan, Coelenterate Mitochondrial
and Mycoplasma/Spiroplasma); 5
(Invertebrate Mitochondrial); 6 (Ciliate
Macronuclear and Dasycladacean); 9
(Echinoderm Mitochondrial); 10 (Euplotid
Nuclear); 11 (Bacterial); 12 (Alternative
Yeast Nuclear); 13 (Ascidian Mitochondrial);
14 (Flatworm Mitochondrial); 15
(Blepharisma Macronuclear); 16
(Chlorophycean Mitochondrial); 21 (Trematode
Mitochondrial); 22 (Scenedesmus obliquus);
23 (Thraustochytrium Mitochondrial))
-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 (Any string)
-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 (Any string)
-sensematch integer [0 - any sense, 1 - forward sense, -1 -
reverse sense] 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 (Integer from -1 to 1)
-minscore float [0.0] Minimum score of feature to display
(see also maxscore) (Any numeric value)
-maxscore float [0.0] Maximum score of feature to display.
If both minscore and maxscore are zero (the
default), then any score is ignored (Any
numeric value)
-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 (Any string)
-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 (Any string)
-stricttags boolean [N] 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.
Advanced (Unprompted) qualifiers:
-mfile datafile [Emethylsites.dat] Restriction enzyme
methylation data file
-flatreformat boolean [N] 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.
-mincuts integer [1] 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. (Integer from 1
to 1000)
-maxcuts integer [2000000000] 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. (Any
integer value)
-sitelen integer [4] This sets the minimum length of the
restriction enzyme recognition site. Any
enzymes with sites shorter than this will be
ignored. (Integer from 2 to 20)
-single boolean [N] 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.
-[no]blunt boolean [Y] This allows those enzymes which cut at
the same position on the forward and reverse
strands to be considered.
-[no]sticky boolean [Y] This allows those enzymes which cut at
different positions on the forward and
reverse strands, leaving an overhang, to be
considered.
-[no]ambiguity boolean [Y] This allows those enzymes which have one
or more 'N' ambiguity codes in their
pattern to be considered
-plasmid boolean [N] 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.
-methylation boolean [N] If this is set then RE recognition sites
will not match methylated bases.
-[no]commercial boolean [Y] 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.
-[no]limit boolean [Y] 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.
-orfminsize integer [0] 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. (Integer 0 or more)
-threeletter boolean [N] Display protein sequences in
three-letter code
-number boolean [N] Number the sequences
-width integer [60] Width of sequence to display (Integer 1
or more)
-length integer [0] Line length of page (0 for indefinite)
(Integer 0 or more)
-margin integer [10] Margin around sequence for numbering
(Integer 0 or more)
-[no]name boolean [Y] Set this to be false if you do not wish
to display the ID name of the sequence
-[no]description boolean [Y] Set this to be false if you do not wish
to display the description of the sequence
-offset integer [1] Offset to start numbering the sequence
from (Any integer value)
-html boolean [N] Use HTML formatting
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-outfile" associated qualifiers
-odirectory2 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit
|
| Qualifier | Type | Description | Allowed values | Default | ||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||||||||||||||||||||||||||||||||
| [-sequence] (Parameter 1) |
seqall | (Gapped) nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | ||||||||||||||||||||||||||||||||||||
| -format | list | Display format |
|
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'. |
|
B,N,T,S,A,F | ||||||||||||||||||||||||||||||||||||
| [-outfile] (Parameter 2) |
outfile | Output file name | Output file | <*>.showseq | ||||||||||||||||||||||||||||||||||||
| Additional (Optional) qualifiers | ||||||||||||||||||||||||||||||||||||||||
| -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 | Sequence range | If this is left blank the complete sequence is translated. | ||||||||||||||||||||||||||||||||||||
| -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 | Sequence range | If this is left blank the complete reverse sequence is translated. | ||||||||||||||||||||||||||||||||||||
| -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 | Sequence range | If this is left blank, then the sequence case is left alone. | ||||||||||||||||||||||||||||||||||||
| -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'. | Sequence range | full sequence | ||||||||||||||||||||||||||||||||||||
| -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'. | Sequence range | If this is left blank, then no annotation is added. | ||||||||||||||||||||||||||||||||||||
| -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 | Any string | all | ||||||||||||||||||||||||||||||||||||
| -table | list | Genetic code to use |
|
0 | ||||||||||||||||||||||||||||||||||||
| -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 | Any string | * | ||||||||||||||||||||||||||||||||||||
| -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 | Any string | * | ||||||||||||||||||||||||||||||||||||
| -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 | Integer from -1 to 1 | 0 - any sense, 1 - forward sense, -1 - reverse sense | ||||||||||||||||||||||||||||||||||||
| -minscore | float | Minimum score of feature to display (see also maxscore) | Any numeric 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 | Any numeric 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 | Any string | * | ||||||||||||||||||||||||||||||||||||
| -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 | Any string | * | ||||||||||||||||||||||||||||||||||||
| -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. | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||||||||||||||||||||||||||||||||
| -mfile | datafile | Restriction enzyme methylation data file | Data file | Emethylsites.dat | ||||||||||||||||||||||||||||||||||||
| -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. | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
| -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. | Integer from 1 to 1000 | 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. | Any integer 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. | Integer from 2 to 20 | 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. | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
| -[no]blunt | boolean | This allows those enzymes which cut at the same position on the forward and reverse strands to be considered. | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -[no]sticky | boolean | This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered. | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -[no]ambiguity | boolean | This allows those enzymes which have one or more 'N' ambiguity codes in their pattern to be considered | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -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. | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
| -methylation | boolean | If this is set then RE recognition sites will not match methylated bases. | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
| -[no]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. | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -[no]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. | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -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. | Integer 0 or more | 0 | ||||||||||||||||||||||||||||||||||||
| -threeletter | boolean | Display protein sequences in three-letter code | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
| -number | boolean | Number the sequences | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
| -width | integer | Width of sequence to display | Integer 1 or more | 60 | ||||||||||||||||||||||||||||||||||||
| -length | integer | Line length of page (0 for indefinite) | Integer 0 or more | 0 | ||||||||||||||||||||||||||||||||||||
| -margin | integer | Margin around sequence for numbering | Integer 0 or more | 10 | ||||||||||||||||||||||||||||||||||||
| -[no]name | boolean | Set this to be false if you do not wish to display the ID name of the sequence | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -[no]description | boolean | Set this to be false if you do not wish to display the description of the sequence | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -offset | integer | Offset to start numbering the sequence from | Any integer value | 1 | ||||||||||||||||||||||||||||||||||||
| -html | boolean | Use HTML formatting | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
| Associated qualifiers | ||||||||||||||||||||||||||||||||||||||||
| "-sequence" associated seqall qualifiers | ||||||||||||||||||||||||||||||||||||||||
| -sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 | ||||||||||||||||||||||||||||||||||||
| -send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 | ||||||||||||||||||||||||||||||||||||
| -sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |||||||||||||||||||||||||||||||||||||
| -sdbname1 -sdbname_sequence |
string | Database name | Any string | |||||||||||||||||||||||||||||||||||||
| -sid1 -sid_sequence |
string | Entryname | Any string | |||||||||||||||||||||||||||||||||||||
| -ufo1 -ufo_sequence |
string | UFO features | Any string | |||||||||||||||||||||||||||||||||||||
| -fformat1 -fformat_sequence |
string | Features format | Any string | |||||||||||||||||||||||||||||||||||||
| -fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |||||||||||||||||||||||||||||||||||||
| "-outfile" associated outfile qualifiers | ||||||||||||||||||||||||||||||||||||||||
| -odirectory2 -odirectory_outfile |
string | Output directory | Any string | |||||||||||||||||||||||||||||||||||||
| General qualifiers | ||||||||||||||||||||||||||||||||||||||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||
| -error | boolean | Report errors | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||||||||||||||||||||||||||||||||
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
Input file format
showseq reads one or more nucleotide sequences.
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
Input files for usage example
'tembl:x13776' is a sequence entry in the example nucleic acid database 'tembl'
Database entry: tembl:x13776
ID X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP.
XX
AC X13776; M43175;
XX
DT 19-APR-1989 (Rel. 19, Created)
DT 14-NOV-2006 (Rel. 89, Last updated, Version 24)
XX
DE Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
XX
KW aliphatic amidase regulator; amiC gene; amiR gene.
XX
OS Pseudomonas aeruginosa
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
XX
RN [1]
RP 1167-2167
RA Rice P.M.;
RT ;
RL Submitted (16-DEC-1988) to the EMBL/GenBank/DDBJ databases.
RL Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
RN [2]
RP 1167-2167
RX DOI; 10.1016/0014-5793(89)80249-2.
RX PUBMED; 2495988.
RA Lowe N., Rice P.M., Drew R.E.;
RT "Nucleotide sequence of the aliphatic amidase regulator gene (amiR) of
RT Pseudomonas aeruginosa";
RL FEBS Lett. 246(1-2):39-43(1989).
XX
RN [3]
RP 1-1292
RX PUBMED; 1907262.
RA Wilson S., Drew R.;
RT "Cloning and DNA sequence of amiC, a new gene regulating expression of the
RT Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
RT product";
RL J. Bacteriol. 173(16):4914-4921(1991).
XX
RN [4]
RP 1-2167
RA Rice P.M.;
RT ;
RL Submitted (04-SEP-1991) to the EMBL/GenBank/DDBJ databases.
RL Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
DR GOA; Q51417.
DR InterPro; IPR003211; AmiSUreI_transpt.
DR UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.
[Part of this file has been deleted for brevity]
FT /replace=""
FT /note="ClaI fragment deleted in pSW36, constitutive
FT phenotype"
FT misc_feature 1
FT /note="last base of an XhoI site"
FT misc_feature 648..653
FT /note="end of 658bp XhoI fragment, deletion in pSW3 causes
FT constitutive expression of amiE"
FT conflict 1281
FT /replace="g"
FT /citation=[3]
XX
SQ Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat 60
ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac 120
aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg 180
aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg 240
agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc 300
ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg 360
tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg 420
agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga 480
acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga 540
ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa 600
gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct 660
acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg 720
cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg 780
ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg 840
aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt 900
acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct 960
tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc 1020
tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt 1080
acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca 1140
gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc 1200
agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt 1260
ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg 1320
cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca 1380
gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt 1440
gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc 1500
gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc 1560
cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga 1620
tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa 1680
gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca 1740
ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct 1800
gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg 1860
aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt 1920
catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg 1980
gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct 2040
gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa 2100
ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt 2160
cctcgag 2167
//
|
You can specify a file of ranges to display in uppercase by giving the '-uppercase' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-upper @myfile').
The format of the range file is:
- Comment lines start with '#' in the first column.
- Comment lines and blank lines are ignored.
- The line may start with white-space.
- There are two positive (integer) numbers per line separated by one or more space or
- TAB characters.
- The second number must be greater or equal to the first number.
- There can be optional text after the two numbers to annotate the line.
- White-space before or after the text is removed.
An example range file is:
# this is my set of ranges 12 23 4 5 this is like 12-23, but smaller 67 10348 interesting region
You can specify a file of ranges to highlight in a different colour when outputting in HTML format (using the '-html' qualifier) by giving the '-highlight' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-highlight @myfile').
The format of this file is very similar to the format of the above
uppercase range file, except that the text after the start and end
positions is used as the HTML colour name. This colour name is used 'as
is' when specifying the colour in HTML in a ''
construct, (where 'xxx' is the name of the colour).
The standard names of HTML font colours are given in
http://http://www.w3.org/TR/REC-html40/types.html#h-6.5
An example highlight range file is:
You can specify a file of ranges to annotate
by giving
the '-annotate' qualifier the value '@' followed by the name of the
file containing the ranges. (eg: '-annotate @myfile').
The format of this file is very similar to the format of the above
highlight range file, except that the text after the start and end
positions is used as the displayed text of the annotated region.
An example annotation range file is:
You can specify a file of enzyme names to read in by giving the
'-enzymes' qualifier 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 '#' or '!' character 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:
Most of the variants of the output format have already been described in
the 'Description' and 'Usage' sections, but here is some more just to
fill out this section ;-)
The output format is extremely variable and under the control of the
qualifiers used.
The sequence can be formatted for HTML display by using the '-html'
qualifier. The top and tail html tags <HEAD>, <BODY> etc. are not
included as it is expected that the output of this program will be
included in a more extensive HTML page and so these parts are left to
the user to provide.
The name of the sequence is displayed, followed by the description of
the sequence. These can be turned off with the '-noname' and
'-nodescription' qualifiers.
Then the sequence is output, one line at a time. Any associated
information to be displayed is also output above and below the sequence
line, as specified by the '-format' and or '-things' qualifiers. (See
the 'Description' section for detals).
The margins around the sequence are specified by the use of the
'-margin' qaulifier and any numbering of the sequence and its
translations are placed in the margin.
A display of the restriction enzyme cut sites can be selected via
'-format 6' option or the '-format 0 -thing b,r,s,-r' style of options.
The option '-format 7' will produce a formatted display of cut sites on
the sequence, with the six-frame translation below it. The cut sites
are indicated by a slash character '\' that points to the poition
between the nucleotides where the cuts occur. Cuts by many enzymes at
the same position are indicated by stacking the enzyme names on top of
each other.
At the end the section header 'Enzymes that cut' is displayed followed
by a list of the enzymes that cut the specified sequence and the number
of times that they cut.
The '-flatreformat' qualifier changes the display to emphasise the
recognition site of the restriction enzyme, which is indicated by a row
of '=' characters. The cut site if pointed to by a '>' or '<' character
and if the cut site is not within or imemdiately adjacent to the
recognition site, they are linked by a row or '.' characters.
The name of the enzyme is displayed above (or below when the reverse
sense site if displayed) the recognition site. The name of the enzyme
is also displayed above the cut site if this occurs on a different
display line to the recognition site (i.e. if it wraps onto the next
line of sequence).
EMBOSS data files are distributed with the application and stored
in the standard EMBOSS data directory, which is defined
by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
Users can provide their own data files in their own directories.
Project specific files can be put in the current directory, or for
tidier directory listings in a subdirectory called
".embossdata". Files for all EMBOSS runs can be put in the user's home
directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
The Genetic Code data files are based on the NCBI genetic code tables.
Their names and descriptions are:
The format of these files is very simple.
It consists of several lines of optional comments, each starting with
a '#' character.
These are followed the line: 'Genetic Code [n]', where 'n' is the
number of the genetic code file.
This is followed by the description of the code and then by four lines
giving the IUPAC one-letter code of the translated amino acid, the
start codons (indicdated by an 'M') and the three bases of the codon,
lined up one on top of the other.
For example:
The EMBOSS REBASE restriction enzyme data files are stored in
directory 'data/REBASE/*' under the EMBOSS installation directory.
These files must first be set up using the program 'rebaseextract'. Running
'rebaseextract' may be the job of your system manager.
The data files are stored in the REBASE directory of the standard EMBOSS
data directory. The names are:
The reported enzyme from any one group of isoschizomers (the prototype)
is specified in the REBASE database and the information is held in the
data file 'embossre.equ'. You may edit this file to set your own
preferred prototype, if you wish.
The format of the file "embossre.equ" is
i.e. two columns of enzyme names separated by a space. The first name
of the pair of enzymes is the name that is not preferred and the second
is the preferred (prototype) name.
One or more things may be selected for display from a menu
(-things option). The order of specified characters (upper
or lower case) determines the order in the output: Alternatively, there is a selection of pre-defined formats to
choose from. The codes from above used in the list of standard formats
are: The default standard format displays the following: for every new
line that the sequence starts to write, the output display will
contain first a blank line (b), then the position numbers of
the ticks (n) then the ticks every 10 characters (t)
then the sequence itself (s) then any user-supplied
annotation (a) then the features from the feature table
(f). Subsequent lines of the sequence output will repeat this
format. The sequence can be translated, using the specified genetic code
tables. The translation can be done in one, three or six frames. The
translation can be displayed in one-letter or three-letter amino acid
codes. The translation can optionally be displayed only when it is in
open reading frames (ORFs) of a specified minimum size. One or more
specified regions of the sequence can be individually translated. The output can be formatted for HTML. If the output is being
formatted for HTML, then specified regions of the sequence can be
displayed in any valid HTML colours. This program can use REBASE data to find the recognition sites
and/or cut sites of restriction enzymes in a nucleic acid sequence.
This program can display the cut sites on both strands.
The -flatreformat option displays not only the cut sites
which many other restriction cut-site programs will show, but also
shows the recognition site. The Restriction Enzyme database (REBASE) is a collection of
information about restriction enzymes and related proteins. It
contains published and unpublished references, recognition and
cleavage sites, isoschizomers, commercial availability, methylation
sensitivity, crystal and sequence data. DNA methyltransferases, homing
endonucleases, nicking enzymes, specificity subunits and control
proteins are also included. Most recently, putative DNA
methyltransferases and restriction enzymes, as predicted from analysis
of genomic sequences, are also listed. The home page of REBASE
is: http://rebase.neb.com/ If the sequence is in EMBL, Genbank or SwissProt format, the
feature table of the sequence can be displayed with the sequence. GFF
file features can also be displayed if they are included on the
command line using -ufo=file.
Other display options include: The displayed sequence can be numbered
either by numbering the start and ending positions, or by placing a
ruler with ticks above or below the sequence. An initial position to
start the numbering from can be set. The width of a line, and width
of a margin around the sequence reserved for numbering can be set.
Specified regions of the sequence can be displayed in uppercase to
highlight them.
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
# this is my set of ranges
12 23 red
4 5 darkturquoise
67 10348 #FFE4E1
# this is my set of ranges
12 23 exon 1
4 5 CAP site
67 10348 exon 2
# my enzymes
HincII, ppiI
# other enzymes
hindiii
HinfI
Output file format
Output files for usage example
File: x13776.showseq
X13776
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation
10 20 30 40 50 60
----:----|----:----|----:----|----:----|----:----|----:----|
ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat
|===============|
promoter note="proposed rpoN-dependent promoter"
|
misc_feature note="last base of an XhoI site"
70 80 90 100
----:----|----:----|----:----|----:----|
ctacctggcgagcctggagcacgagcgggttcgcttcgta
|===============|
promoter note="proposed rpoN-dependent promoter"
Output files for usage example 2
File: x13776.showseq
X13776
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation
ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat
----:----|----:----|----:----|----:----|----:----|----:----|
ccatggcgaccggctcgtagacgagctagtggtggtcggcccgctgcccttgacgtgcta
ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac
----:----|----:----|----:----|----:----|----:----|----:----|
gatggaccgctcggacctcgtgctcgcccaagcgaagcatgccgcgactcgctgtcagtg
Output files for usage example 3
File: x13776.showseq
ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat
ctacctggcgagcctggagcacgagcgggttcgcttcgta
Output files for usage example 4
File: x13776.showseq
X13776
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation
1 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat 60
61 ctacctggcgagcctggagcacgagcgggttcgcttcgta 100
Output files for usage example 5
File: x13776.showseq
X13776
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation
123 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat 182
183 ctacctggcgagcctggagcacgagcgggttcgcttcgta 222
Output files for usage example 6
File: x13776.showseq
X13776
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation
ggtaccgCTGGCCGAGCATCTGCTcgatcaccaccagccgggcgacgggaactgcacgat
ctacCTGGCGAGCCTGGAGCAcgagcgggttcgcttcgta
Output files for usage example 7
File: x13776.showseq
X13776
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation
10 20 30 40 50 60
----:----|----:----|----:----|----:----|----:----|----:----|
ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat
R S P P A G R R V
|===============|
promoter note="proposed rpoN-dependent promoter"
|
misc_feature note="last base of an XhoI site"
70 80 90 100 110 120
----:----|----:----|----:----|----:----|----:----|----:----|
ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac
A S L
|===============|
promoter note="proposed rpoN-dependent promoter"
Output files for usage example 8
File: x13776.showseq
X13776
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation
10 20 30 40 50 60
----:----|----:----|----:----|----:----|----:----|----:----|
ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat
|------------|
binding site
|
SNP
|===============|
promoter note="proposed rpoN-dependent promoter"
|
misc_feature note="last base of an XhoI site"
70 80 90 100 110 120
----:----|----:----|----:----|----:----|----:----|----:----|
ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac
|===============|
promoter note="proposed rpoN-dependent promoter"
Data files
% embossdata -showall
% embossdata -fetch -file Exxx.dat
------------------------------------------------------------------------------
# Genetic Code Table
#
# Obtained from: http://www.ncbi.nlm.nih.gov/collab/FT/genetic_codes.html
# and: http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c
#
# Differs from Genetic Code [1] only in that the initiation sites have been
# changed to only 'AUG'
Genetic Code [0]
Standard
AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
------------------------------------------------------------------------------
The column information is described at the top of the data files
Enzyme-name Prototype-name
Notes
s Sequence
b Blank line
1 Frame 1 translation
2 Frame 2 translation
3 Frame 3 translation
-1 Frame -1 translation
-2 Frame -2 translation
-2 Frame -3 translation
t Ticks line
n Number ticks line
c Complement sequence
f Features (from the feature table or from a command line -ufo file)
r Restriction enzyme cut sites in the forward sense
-r Restriction enzyme cut sites in the reverse sense
a User Annotation
Sequence only: S A
Default sequence: B N T S A F
Pretty sequence: B N T S A
One frame translation: B N T S B 1 A F
Three frame translations: B N T S B 1 2 3 A F
Six frame translations: B N T S B 1 2 3 T -3 -2 -1 A F
Restriction enzyme map: B R S N T C -R B 1 2 3 T -3 -2 -1 A
Baroque: B 1 2 3 N T R S T C -R T -3 -2 -1 A F
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None known.
See also
Program name
Description
backtranambig
Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq
Back-translate a protein sequence to a nucleotide sequence
checktrans
Reports STOP codons and ORF statistics of a protein
coderet
Extract CDS, mRNA and translations from feature tables
plotorf
Plot potential open reading frames in a nucleotide sequence
prettyseq
Write a nucleotide sequence and its translation to file
recoder
Find restriction sites to remove (mutate) with no translation change
redata
Retrieve information from REBASE restriction enzyme database
remap
Display restriction enzyme binding sites in a nucleotide sequence
restover
Find restriction enzymes producing a specific overhang
restrict
Report restriction enzyme cleavage sites in a nucleotide sequence
showorf
Display a nucleotide sequence and translation in pretty format
silent
Find restriction sites to insert (mutate) with no translation change
sixpack
Display a DNA sequence with 6-frame translation and ORFs
transeq
Translate nucleic acid sequences
Author(s)
Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
History
Written 1999 - GWW
23 Aug 2000 - features display added - GWW
20 Nov 2001 - feature matches and annotation display added - GWW
16 Dec 2008 - limited to nucleotide only. Use showpep for proteins - PMR
Target users
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
Comments
None