Required section¶
-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
-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
Advanced section¶
-min 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
-max 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
-solofragment boolean
This gives the fragment lengths of the forward sense
strand produced by complete restriction by each restriction enzyme on its own.
Results are added to the tail section of the report. Default value: N
-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
Output section¶
-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
-alphabetic boolean
Default value: N
-fragments boolean
This gives the fragment lengths of the forward sense
strand produced by complete restriction using all of the input enzymes
together. Results are added to the tail section of the report. Default value:
N
-name boolean
Default value: N
-outfile report
