OPTIONS¶
-sequence seqall
-mfile datafile
Default value: Emethylsites.dat
Required section¶
-enzymes string
The name 'all' reads in all enzyme names from the REBASE
database. You can specify enzymes by giving their names with commas between
then, such as: 'HincII,hinfI,ppiI,hindiii'. The case of the names is not
important. You can specify a file of enzyme names to read in by giving the
name of the file holding the enzyme names with a '@' character in front of it,
for example, '@enz.list'. Blank lines and lines starting with a hash character
or '!' are ignored and all other lines are concatenated together with a comma
character ',' and then treated as the list of enzymes to search for. An
example of a file of enzyme names is: ! my enzymes HincII, ppiII ! other
enzymes hindiii HinfI PpiI Default value: all
-sitelen integer
This sets the minimum length of the restriction enzyme
recognition site. Any enzymes with sites shorter than this will be ignored.
Default value: 4
Additional section¶
-mincuts integer
This sets the minimum number of cuts for any restriction
enzyme that will be considered. Any enzymes that cut fewer times than this
will be ignored. Default value: 1
-maxcuts integer
This sets the maximum number of cuts for any restriction
enzyme that will be considered. Any enzymes that cut more times than this will
be ignored. Default value: 2000000000
-single boolean
If this is set then this forces the values of the mincuts
and maxcuts qualifiers to both be 1. Any other value you may have set them to
will be ignored. Default value: N
-blunt boolean
This allows those enzymes which cut at the same position
on the forward and reverse strands to be considered. Default value: Y
-sticky boolean
This allows those enzymes which cut at different
positions on the forward and reverse strands, leaving an overhang, to be
considered. Default value: Y
-ambiguity boolean
This allows those enzymes which have one or more 'N'
ambiguity codes in their pattern to be considered Default value: Y
-plasmid boolean
If this is set then this allows searches for restriction
enzyme recognition site and cut positions that span the end of the sequence to
be considered. Default value: N
-methylation boolean
If this is set then RE recognition sites will not match
methylated bases. Default value: N
-commercial boolean
If this is set, then only those enzymes with a commercial
supplier will be searched for. This qualifier is ignored if you have specified
an explicit list of enzymes to search for, rather than searching through 'all'
the enzymes in the REBASE database. It is assumed that, if you are asking for
an explicit enzyme, then you probably know where to get it from and so all
enzymes names that you have asked to be searched for, and which cut, will be
reported whether or not they have a commercial supplier. Default value:
Y
-table list
-frame list
This allows you to specify the frames that are
translated. If you are not displaying cut sites on the reverse sense, then the
reverse sense translations will not be displayed even if you have requested
frames 4, 5 or 6. By default, all six frames will be displayed. Default value:
6
Output section¶
-outfile outfile
-cutlist boolean
This produces lists in the output of the enzymes that
cut, those that cut but are excluded because that cut fewer times than mincut
or more times than maxcut and those enzymes that do not cut. Default value:
Y
-flatreformat boolean
This changes the output format to one where the
recognition site is indicated by a row of '===' characters and the cut site is
pointed to by a '>' character in the forward sense, or a '<' in the
reverse sense strand. Default value: N
-limit boolean
This limits the reporting of enzymes to just one enzyme
from each group of isoschizomers. The enzyme chosen to represent an
isoschizomer group is the prototype indicated in the data file 'embossre.equ',
which is created by the program 'rebaseextract'. If you prefer different
prototypes to be used, make a copy of embossre.equ in your home directory and
edit it. If this value is set to be false then all of the input enzymes will
be reported. You might like to set this to false if you are supplying an
explicit set of enzymes rather than searching 'all' of them. Default value:
Y
-translation boolean
This displays the 6-frame translations of the sequence in
the output. Default value: Y
-reverse boolean
This displays the cut sites and translation of the
reverse sense. Default value: Y
-orfminsize integer
This sets the minimum size of Open Reading Frames (ORFs)
to display in the translations. All other translation regions are masked by
changing the amino acids to '-' characters.
-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'.
-threeletter boolean
Default value: N
-number boolean
Default value: N
-width integer
Default value: 60
-length integer
-margin integer
Default value: 10
-name boolean
Set this to be false if you do not wish to display the ID
name of the sequence Default value: Y
-description boolean
Set this to be false if you do not wish to display the
description of the sequence Default value: Y
-offset integer
Default value: 1
-html boolean
Default value: N
