|
showseq |
Function
Display a sequence with features, translation etcDescription
showseq displays a protein or a nucleic acid sequence in a style suitable for publication.The output is sent to the screen by default for the user to view, but it can write the results to a file.
The display style of the output is very flexible. The user can select a style from the pre-set choice of formats, or can design a style to suit their purposes and aesthetic tastes.
If designing a new format, you can choose the order in which things are printed around the sequence. The things that you can display are:
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
The letters for these things can be in upper or lower case.
They can be displayed in any order.
You do not have to make your own format; there is a selection of pre-defined standard formats for you to choose from.
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 'thing' codes used in the list of standard formats are:
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
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.
The width of a line can be set. The width of a margin around the sequence reserved for numbering can be set. The initial position to start numbering from can be set.
The sequence can be translated, using the selectable 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.
Specified regions of the sequence can be displayed in uppercase to highlight them.
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.
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/
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.
One potentially very useful option is '-flatreformat' that displays not only the cut sites which many other restriction cut-site programs will show, but also shows the recognition site.
If the sequence is in EMBL, Genbank or SwissProt format, the feature table of the sequence can be dispalyed with the sequence. GFF file features can also be displayed if they are included on the command line with the -ufo=file qualifier.
Usage
Here is a sample session with showseq
% showseq tembl:paamir -sbeg 1 -send 100
Display a sequence with features, translation etc..
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 [paamir.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:paamir -sbeg 1 -send 120
Display a sequence with features, translation etc..
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 [paamir.showseq]:
|
Go to the output files for this example
Example 3
Display only the sequence:
% showseq tembl:paamir -sbeg 1 -send 100 -noname -nodesc -format 0 -thing S Display a sequence with features, translation etc.. Output file [paamir.showseq]: |
Go to the output files for this example
Example 4
Protein sequence can be displayed in three-letter codes. (The codes are displayed downwards, so the first code is 'Met'):
% showseq tsw:rs24_fugru -three -format 2 Display a sequence with features, translation etc.. Output file [rs24_fugru.showseq]: |
Go to the input files for this example
Go to the output files for this example
Example 5
Number the sequence lines in the margin:
% showseq tembl:paamir -sbeg 1 -send 100 -format 1 -number Display a sequence with features, translation etc.. Output file [paamir.showseq]: |
Go to the output files for this example
Example 6
Start the numbering at a specified value ('123' in this case):
% showseq tembl:paamir -sbeg 1 -send 100 -format 1 -number -offset 123 Display a sequence with features, translation etc.. Output file [paamir.showseq]: |
Go to the output files for this example
Example 7
Make selected regions uppercase. (Use '-slower' to force the rest of the sequence to be lowercase).
% showseq tembl:paamir -sbeg 1 -send 100 -format 1 -slower -upper '25-45,101-203,333-362' Display a sequence with features, translation etc.. Output file [paamir.showseq]: |
Go to the output files for this example
Example 8
Translate selected regions:
% showseq tembl:paamir -sbeg 1 -send 120 -format 4 -trans 25-49,66-76 Display a sequence with features, translation etc.. Output file [paamir.showseq]: |
Go to the output files for this example
Example 9
Add your own annotation to the display:
% showseq tembl:paamir -sbeg 1 -send 100 -format 2 -send 120 -annotation '13-26 binding site 15-15 SNP' Display a sequence with features, translation etc.. Output file [paamir.showseq]: |
Go to the output files for this example
Command line arguments
Standard (Mandatory) qualifiers (* if not always prompted):
[-sequence] seqall Sequence database USA
-format menu Display format
* -things menu 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'.
[-outfile] outfile Output file name
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
1,5,8,10,23,45,57,99
-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
-table menu Genetic code to use
-matchsource 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
-matchtype 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://www3.ebi.ac.uk/Services/WebFeat/
for a list of the EMBL feature types and see
Appendix A of the Swissprot user manual in
http://www.expasy.ch/txt/userman.txt 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
-matchsense 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 If this is greater than or equal to the
maximum score, then any score is permitted
-maxscore float If this is less than or equal to the maximum
score, then any score is permitted
-matchtag 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
-matchvalue 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 valueyou 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
-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.
Advanced (Unprompted) qualifiers:
-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.
-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.
-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.
-sitelen integer This sets the minimum length of the
restriction enzyme recognition site. Any
enzymes with sites shorter than this will be
ignored.
-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.
-[no]blunt boolean This allows those enzymes which cut at the
same position on the forward and reverse
strands to be considered.
-[no]sticky boolean This allows those enzymes which cut at
different positions on the forward and
reverse strands, leaving an overhang, to be
considered.
-[no]ambiguity boolean This allows those enzymes which have one or
more 'N' ambiguity codes in their pattern to
be considered
-plasmid boolean If this is set then this allows searches for
restriction enzyme recognition site and cut
postions that span the end of the sequence
to be considered.
-[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.
-[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.
-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 Display protein sequences in three-letter
code
-number boolean Number the sequences
-width integer Width of sequence to display
-length integer Line length of page (0 for indefinite)
-margin integer Margin around sequence for numbering
-[no]name boolean Set this to be false if you do not wish to
display the ID name of the sequence
-[no]description boolean Set this to be false if you do not wish to
display the description of the sequence
-offset integer Offset to start numbering the sequence from
-html boolean 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 standard output
-filter boolean Read standard input, write 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. 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 deaths
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| Standard (Mandatory) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required | ||||||||||||||||||||||||||||||||||||
| -format | Display format |
|
2 | ||||||||||||||||||||||||||||||||||||
| -things | 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) |
Output file name | Output file | <sequence>.showseq | ||||||||||||||||||||||||||||||||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
| -translate | 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 1,5,8,10,23,45,57,99 | Sequence range | If this is left blank the complete sequence is translated. | ||||||||||||||||||||||||||||||||||||
| -uppercase | 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 | 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 | 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 | 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 is accepted | all | ||||||||||||||||||||||||||||||||||||
| -table | Genetic code to use |
|
0 | ||||||||||||||||||||||||||||||||||||
| -matchsource | 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 is accepted | * | ||||||||||||||||||||||||||||||||||||
| -matchtype | 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://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt 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 is accepted | * | ||||||||||||||||||||||||||||||||||||
| -matchsense | 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 | Any integer value | 0 - any sense, 1 - forward sense, -1 - reverse sense | ||||||||||||||||||||||||||||||||||||
| -minscore | If this is greater than or equal to the maximum score, then any score is permitted | Any numeric value | 0.0 | ||||||||||||||||||||||||||||||||||||
| -maxscore | If this is less than or equal to the maximum score, then any score is permitted | Any numeric value | 0.0 | ||||||||||||||||||||||||||||||||||||
| -matchtag | 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 is accepted | * | ||||||||||||||||||||||||||||||||||||
| -matchvalue | 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 valueyou 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 is accepted | * | ||||||||||||||||||||||||||||||||||||
| -stricttags | 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 | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
| -flatreformat | 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 | 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 | 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. | Integer up to 2000000000 | 2000000000 | ||||||||||||||||||||||||||||||||||||
| -sitelen | 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 | 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 | 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 | 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 | This allows those enzymes which have one or more 'N' ambiguity codes in their pattern to be considered | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -plasmid | If this is set then this allows searches for restriction enzyme recognition site and cut postions that span the end of the sequence to be considered. | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
| -[no]commercial | 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 | 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 | 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 | Display protein sequences in three-letter code | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
| -number | Number the sequences | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
| -width | Width of sequence to display | Integer 1 or more | 60 | ||||||||||||||||||||||||||||||||||||
| -length | Line length of page (0 for indefinite) | Integer 0 or more | 0 | ||||||||||||||||||||||||||||||||||||
| -margin | Margin around sequence for numbering | Integer 0 or more | 10 | ||||||||||||||||||||||||||||||||||||
| -[no]name | 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 | Set this to be false if you do not wish to display the description of the sequence | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -offset | Offset to start numbering the sequence from | Any integer value | 1 | ||||||||||||||||||||||||||||||||||||
| -html | Use HTML formatting | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
Input file format
showseq reads normal sequence USAs.Input files for usage example
'tembl:paamir' is a sequence entry in the example nucleic acid database 'tembl'
Database entry: tembl:paamir
ID PAAMIR standard; DNA; PRO; 2167 BP.
XX
AC X13776; M43175;
XX
SV X13776.1
XX
DT 19-APR-1989 (Rel. 19, Created)
DT 17-FEB-1997 (Rel. 50, Last updated, Version 22)
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; gamma subdivision; 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 MEDLINE; 89211409.
RA Lowe N., Rice P.M., Drew R.E.;
RT "Nucleotide sequence of the aliphatic amidase regulator gene of Pseudomonas
RT aeruginosa";
RL FEBS Lett. 246:39-43(1989).
XX
RN [3]
RP 1-1292
RX MEDLINE; 91317707.
RA Wilson S., Drew R.;
RT "Cloning and DNA seqence of amiC, a new gene regulating expression of the
RT Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
RT product.";
RL J. Bacteriol. 173:4914-4921(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 SWISS-PROT; P10932; AMIR_PSEAE.
DR SWISS-PROT; P27017; AMIC_PSEAE.
DR SWISS-PROT; Q51417; AMIS_PSEAE.
[Part of this file has been deleted for brevity]
FT phenotype"
FT /replace=""
FT /gene="amiC"
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
//
|
Input files for usage example 4
'tsw:rs24_fugru' is a sequence entry in the example protein database 'tsw'
Database entry: tsw:rs24_fugru
ID RS24_FUGRU STANDARD; PRT; 132 AA.
AC O42387;
DT 15-JUL-1998 (REL. 36, CREATED)
DT 15-JUL-1998 (REL. 36, LAST SEQUENCE UPDATE)
DT 15-JUL-1998 (REL. 36, LAST ANNOTATION UPDATE)
DE 40S RIBOSOMAL PROTEIN S24.
GN RPS24.
OS FUGU RUBRIPES (JAPANESE PUFFERFISH) (TAKIFUGU RUBRIPES).
OC EUKARYOTA; METAZOA; CHORDATA; VERTEBRATA; PISCES; GNATHOSTOMATA;
OC OSTEICHTHYES; ACTINOPTERYGII; TETRAODONTIFORMES.
RN [1]
RP SEQUENCE FROM N.A.
RA CROSIO C., CECCONI F., GIORGI M., AMALDI F., MARIOTTINI P.;
RL SUBMITTED (SEP-1997) TO EMBL/GENBANK/DDBJ DATA BANKS.
CC -!- SIMILARITY: BELONGS TO THE S24E FAMILY OF RIBOSOMAL PROTEINS.
DR EMBL; AJ001398; E339629; -.
DR PROSITE; PS00529; RIBOSOMAL_S24E; 1.
KW RIBOSOMAL PROTEIN.
SQ SEQUENCE 132 AA; 15305 MW; BCF9EB31 CRC32;
MNDTVTVRTR KFMTNRLLQR KQMVVDVLHP GKATVPKTEI REKLAKMYKT TPDVVFVFGF
RTQFGGGKTT GFAMVYDSLD YAKKNEPKHR LARHGLFEKK KTSRKQRKER KNRMKKVRGT
KKASVGASKK KD
//
|
You can specifiy 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 specifiy 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:
An example highlight range file is:
You can specifiy 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 iin
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.
If you ask for the sequence display to end at position '100', with the
qualifier '-send 100', it will display the sequence up to the end of the
line - position '120'. This is a feature of this program to make the
display of things like restriction enzyme cutting sites easier.
It is not a bug. Please don't report it.
http://http://www.w3.org/TR/REC-html40/types.html
and
http://www.ausmall.com.au/freegraf/ncolour2.htm
and
http://mindprod.com/htmlcolours.html
(amongst other places).
# 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
Note that although we asked for the sequence display to end at position '100', it has displayed the sequence up to the end of the line - position '120'. This is a feature of this program to make the display of things like restriction enzyme cutting sites easier. File: paamir.showseq
PAAMIR
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 90 100 110 120
----:----|----:----|----:----|----:----|----:----|----:----|
ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac
|===============|
promoter note="proposed rpoN-dependent promoter"
Output files for usage example 2
File: paamir.showseq
PAAMIR
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation
ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat
----:----|----:----|----:----|----:----|----:----|----:----|
ccatggcgaccggctcgtagacgagctagtggtggtcggcccgctgcccttgacgtgcta
ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac
----:----|----:----|----:----|----:----|----:----|----:----|
gatggaccgctcggacctcgtgctcgcccaagcgaagcatgccgcgactcgctgtcagtg
Output files for usage example 3
File: paamir.showseq
ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat
ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac
Output files for usage example 4
File: rs24_fugru.showseq
RS24_FUGRU
40S RIBOSOMAL PROTEIN S24.
10 20 30 40 50 60
----:----|----:----|----:----|----:----|----:----|----:----|
MAATVTVATALPMTAALLGALGMVVAVLHPGLATVPLTGIAGLLALMTLTTPAVVPVPGP
esshaharhryhehsreelryleaasaeirlylharyhllrlyelyeyyhhrsaahahlh
tnprlrlgrgsetrnguungsntllplusoysarlosruegusuastrsrroplleleye
70 80 90 100 110 120
----:----|----:----|----:----|----:----|----:----|----:----|
ATGPGGGLTTGPAMVTASLATALLAGPLHALAAHGLPGLLLTSALGALGALAAMLLVAGT
rhlhlllyhhlhleayseesylyyslryirelrilehlyyyherylrylrysreyyarlh
grneyyysrryeatlrpruprassnuossguagsyueusssrrgsngsugsngtsslgyr
130 140 150 160 170 180
----:----|----:----|----:----|----:----|----:----|----:----|
LLASVGASLLLA
yylealleyyys
ssarlyarsssp
Output files for usage example 5
File: paamir.showseq
PAAMIR
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation
1 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat 60
61 ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac 120
Output files for usage example 6
File: paamir.showseq
PAAMIR
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation
123 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat 182
183 ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac 242
Output files for usage example 7
File: paamir.showseq
PAAMIR
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation
ggtaccgctggccgagcatctgctCGATCACCACCAGCCGGGCGAcgggaactgcacgat
ctacctggcgagcctggagcacgagcgggttcgcttcgtaCGGCGCTGAGCGACAGTCAC
Output files for usage example 8
File: paamir.showseq
PAAMIR
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 9
File: paamir.showseq
PAAMIR
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
None.
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 abiview Reads ABI file and display the trace backtranseq Back translate a protein sequence cirdna Draws circular maps of DNA constructs coderet Extract CDS, mRNA and translations from feature tables lindna Draws linear maps of DNA constructs pepnet Displays proteins as a helical net pepwheel Shows protein sequences as helices plotorf Plot potential open reading frames prettyplot Displays aligned sequences, with colouring and boxing prettyseq Output sequence with translated ranges recoder Remove restriction sites but maintain same translation redata Search REBASE for enzyme name, references, suppliers etc remap Display sequence with restriction sites, translation etc restover Find restriction enzymes producing specific overhang restrict Finds restriction enzyme cleavage sites seealso Finds programs sharing group names showalign Displays a multiple sequence alignment showdb Displays information on the currently available databases showfeat Show features of a sequence showorf Pretty output of DNA translations silent Silent mutation restriction enzyme scan sixpack Display a DNA sequence with 6-frame translation and ORFs textsearch Search sequence documentation. Slow, use SRS and Entrez! transeq Translate nucleic acid sequences
Author(s)
Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
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
Target users
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
Comments
None