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PROGRAM:

NAME

remap - Display restriction enzyme binding sites in a nucleotide sequence

SYNOPSIS

remap -sequence seqall -mfile datafile -enzymes string -sitelen integer [-mincuts integer]
[-maxcuts integer] [-single boolean] [-blunt boolean] [-sticky boolean]
[-ambiguity boolean] [-plasmid boolean] [-methylation boolean] [-commercial boolean]
[-table list] [-frame list] -outfile outfile [-cutlist boolean]
[-flatreformat boolean] [-limit boolean] -translation boolean -reverse boolean
-orfminsize integer -uppercase range -highlight range -threeletter boolean
-number boolean -width integer -length integer -margin integer -name boolean
-description boolean -offset integer -html boolean

remap -help

DESCRIPTION

remap is a command line program from EMBOSS (“the European Molecular Biology Open Software
Suite”). It is part of the "Display,Nucleic:Restriction,Nucleic:Translation" command
group(s).

OPTIONS

Input section
-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

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