remap uses REBASE data to find the recognition sites and/or cut sites of restriction enzymes in a nucleic acid sequence. It also displays the cut sites on both strands by default. It will optionally also display the translation of the sequence.
Here is a sample session with remap. We only look at a small section of the sequence to save space:
% remap -notran -sbeg 1 -send 60 Display a sequence with restriction cut sites, translation etc.. Input sequence(s): embl:eclac Output file [eclac.remap]: Comma separated enzyme list [all]: taqi,bsu6i,acii,bsski Minimum recognition site length :
Here is an example where all enzymes in the REBASE database are used:
% remap -notran -sbeg 1 -send 60 Display a sequence with restriction cut sites, translation etc.. Input sequence(s): embl:eclac Output file [eclac.remap]: Comma separated enzyme list [all]: Minimum recognition site length :
- [-sequence] (seqall)
Sequence database USA.
- -enzymes (string)
The argument all reads all enzyme names from the REBASE database. You can specify enzymes by giving their names with commas between them, such as: HincII,hinfI,ppiI,hindiii. This command is not case-sensitive. You may also use the data from file containing enzyme names by prepending the name of the file you want to use with an @ character; for example, @enz.list. Blank lines and lines starting with a comment tag (# or !) within the file are ignored; all other lines are concatenated together with a comma and treated as the list of enzymes to search for. A file containing enzyme names might look like this:
! my enzymes HincII, ppiII ! other enzymes hindiii HinfI PpiI
- -sitelen (integer)
Minimum recognition site length.
- [-outfile] (outfile)
If you enter the name of a file here, this program will write the sequence details into that file.
- -mincuts (integer)
Minimum cuts per restriction enzyme.
- -maxcuts (integer
Maximum cuts per restriction enzyme.
- -single (boolean)
Force single-site-only cuts.
- -[no]blunt (boolean)
Allow blunt end cutters.
- -[no]sticky (boolean)
Allow sticky end cutters.
- -[no]ambiguity (boolean)
Allow ambiguous matches.
- -plasmid (boolean)
Allow circular DNA.
- -[no]commercial (boolean)
Only enzymes with suppliers.
- -table (menu)
Code to use. See the fuzztran description for codes.
- -[no]cutlist (boolean)
List the enzymes to cut.
- -flatreformat (boolean)
Display restriction enzyme sites in flat format.
- -[no]limit (boolean)
Limits reports to one isoschizomer.
- -preferred (boolean)
Report preferred isoschizomers.
- -[no]translation (boolean)
- -[no]reverse (boolean)
Display cut sites and translation of reverse sense.
- -orfminsize (integer)
Minimum size of Open Reading Frames (ORFs) to display in the translations.
- -uppercase (range)
Regions to put in uppercase. If no regions are specified, 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 specification: 24-45, 56-78, 1:45, 67=99;765..888, 1,5,8,10,23,45,57,99.
- -highlight (range)
Regions to color if formatting in HTML. If no regions are specified, 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 color. Examples of region specifications:
24-45 blue 56-78 orange 1-100 green 120-156 red
A file of ranges to color (one range per line) can be specifed as @filename.
- -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 length).
- -margin (integer)
Margin around sequence for numbering.
- -[no]name (boolean)
Set this to false if you do not want to display the ID name of the sequence.
- -[no]description (boolean)
Set this to false if you do not want to display the description of the sequence.
- -offset (integer)
Offset to start numbering the sequence from.
- -html (boolean)
Use HTML formatting.