Inputsection-sequenceseqall-mfiledatafile
Default value: Emethylsites.dat
Requiredsection-formatlist
Default value: 2
-thingslist
Specify a list of one or more code characters in the order in which you wish things to be displayed
one above the other down the page. For example if you wish to see things displayed in the order:
sequence, complement sequence, ticks line, frame 1 translation, blank line; then you should enter
'S,C,T,1,B'. Default value: B,N,T,S,A,F
Additionalsection-translaterange
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
-revtranslaterange
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
-uppercaserange
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
-highlightrange
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'.
-annotationrange
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'.
-enzymesstring
The name 'all' reads in all enzyme names from the REBASE database. You can specify enzymes by giving
their names with commas between then, such as: 'HincII,hinfI,ppiI,hindiii'. The case of the names is
not important. You can specify a file of enzyme names to read in by giving the name of the file
holding the enzyme names with a '@' character in front of it, for example, '@enz.list'. Blank lines
and lines starting with a hash character or '!' are ignored and all other lines are concatenated
together with a comma character ',' and then treated as the list of enzymes to search for. An example
of a file of enzyme names is: ! my enzymes HincII, ppiII ! other enzymes hindiii HinfI PpiI Default
value: all
-tablelistFeaturedisplayoptions-sourcematchstring
By default any feature source in the feature table is shown. You can set this to match any feature
source you wish to show. The source name is usually either the name of the program that detected the
feature or it is the feature table (eg: EMBL) that the feature came from. The source may be
wildcarded by using '*'. If you wish to show more than one source, separate their names with the
character '|', eg: gene* | embl Default value: *
-typematchstring
By default any feature type in the feature table is shown. You can set this to match any feature type
you wish to show. See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see
Appendix A of the Swissprot user manual in http://www.expasy.org/sprot/userman.html for a list of the
Swissprot feature types. The type may be wildcarded by using '*'. If you wish to show more than one
type, separate their names with the character '|', eg: *UTR | intron Default value: *
-sensematchinteger
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
-minscorefloat
Minimum score of feature to display (see also maxscore) Default value: 0.0
-maxscorefloat
Maximum score of feature to display. If both minscore and maxscore are zero (the default), then any
score is ignored Default value: 0.0
-tagmatchstring
Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a
'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number',
'/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial',
'/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except',
'/transl_table', or '/usedin'. Some of these tags also have values, for example '/gene' can have the
value of the gene name. By default any feature tag in the feature table is shown. You can set this to
match any feature tag you wish to show. The tag may be wildcarded by using '*'. If you wish to show
more than one tag, separate their names with the character '|', eg: gene | label Default value: *
-valuematchstring
Tag values are the values associated with a feature tag. Tags are the types of extra values that a
feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags
'/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene',
'/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo',
'/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Only some of these
tags can have values, for example '/gene' can have the value of the gene name. By default any feature
tag value in the feature table is shown. You can set this to match any feature tag value you wish to
show. The tag value may be wildcarded by using '*'. If you wish to show more than one tag value,
separate their names with the character '|', eg: pax* | 10 Default value: *
-stricttagsboolean
By default if any tag/value pair in a feature matches the specified tag and value, then all the
tags/value pairs of that feature will be displayed. If this is set to be true, then only those
tag/value pairs in a feature that match the specified tag and value will be displayed. Default value:
N
AdvancedsectionRestrictionmapoptions-flatreformatboolean
This changes the output format to one where the recognition site is indicated by a row of '==='
characters and the cut site is pointed to by a '>' character in the forward sense, or a '<' in the
reverse sense strand. Default value: N
-mincutsinteger
This sets the minimum number of cuts for any restriction enzyme that will be considered. Any enzymes
that cut fewer times than this will be ignored. Default value: 1
-maxcutsinteger
This sets the maximum number of cuts for any restriction enzyme that will be considered. Any enzymes
that cut more times than this will be ignored. Default value: 2000000000
-siteleninteger
This sets the minimum length of the restriction enzyme recognition site. Any enzymes with sites
shorter than this will be ignored. Default value: 4
-singleboolean
If this is set then this forces the values of the mincuts and maxcuts qualifiers to both be 1. Any
other value you may have set them to will be ignored. Default value: N
-bluntboolean
This allows those enzymes which cut at the same position on the forward and reverse strands to be
considered. Default value: Y
-stickyboolean
This allows those enzymes which cut at different positions on the forward and reverse strands,
leaving an overhang, to be considered. Default value: Y
-ambiguityboolean
This allows those enzymes which have one or more 'N' ambiguity codes in their pattern to be
considered Default value: Y
-plasmidboolean
If this is set then this allows searches for restriction enzyme recognition site and cut positions
that span the end of the sequence to be considered. Default value: N
-methylationboolean
If this is set then RE recognition sites will not match methylated bases. Default value: N
-commercialboolean
If this is set, then only those enzymes with a commercial supplier will be searched for. This
qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than
searching through 'all' the enzymes in the REBASE database. It is assumed that, if you are asking for
an explicit enzyme, then you probably know where to get it from and so all enzymes names that you
have asked to be searched for, and which cut, will be reported whether or not they have a commercial
supplier. Default value: Y
-limitboolean
This limits the reporting of enzymes to just one enzyme from each group of isoschizomers. The enzyme
chosen to represent an isoschizomer group is the prototype indicated in the data file 'embossre.equ',
which is created by the program 'rebaseextract'. If you prefer different prototypes to be used, make
a copy of embossre.equ in your home directory and edit it. If this value is set to be false then all
of the input enzymes will be reported. You might like to set this to false if you are supplying an
explicit set of enzymes rather than searching 'all' of them. Default value: Y
-orfminsizeinteger
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.
-threeletterboolean
Default value: N
-numberboolean
Default value: N
-widthinteger
Default value: 60
-lengthinteger-margininteger
Default value: 10
-nameboolean
Set this to be false if you do not wish to display the ID name of the sequence Default value: Y
-descriptionboolean
Set this to be false if you do not wish to display the description of the sequence Default value: Y
-offsetinteger
Default value: 1
-htmlboolean
Default value: N
Outputsection-outfileoutfile
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