MAP displays both strands of a DNA sequence, restriction sites, and protein translation(s).
MAPSORT lists cut-positions and fragment sizes, OR makes a complete digest, sorting the fragments. OR, with PLASMIDMAP, it can be used to create a detailed graphical display.
MAPPLOT shows an overview of the restriction sites.
Use MAP without any command-line modifiers, to show ALL possible enzymes and ALL possible cut sites.
$ Map
(Linear) MAP of what sequence? Platelet.seq
Begin (* 1 *) ?
End (* 1308 *) ?
. {output
omitted}
Enzyme (* * *):
{Press return to select all the enzymes in the list}
Please select (capitalise for 3-letter) (* t *) AO
What should I call the output file (* Platelet.map *)
Entry of 'AO' shows the protein translation in the first frame only for the open reading frame. Type the output file:
$ Type platelet.map
To show the restriction sites of enzymes that cut ONLY twice: /mincuts=2 defines a minimum number of cuts, and /maxcuts=2 defines a maximum number.
$Map/mincuts=2/maxcuts=2
(Linear) MAP of what sequence? Platelet.seq
Begin (* 1 *) ?
End (* 1308 *) ?
Enzyme (* * *):
{Press return to select all the enzymes in the list}
Please select (capitalise for 3-letter) (* t *) ao
What should I call the output file (* Platelet.map *)
'ao' in lower case shows the single letter protein translation.
Type the output file platelet.map.
We can limit the identification of restriction sites in other ways. Using /exclude on the command line, we can identify restriction sites that DO NOT OCCUR in the excluded region (qv: the open reading frame region is 388 to 1020). /Six selects enzymes with six or more bases in the recognition site.
$ Mapsort/exclude=388,1020/sixbase
(Linear) (Six-base) MAPSORT of what sequence ? platelet.seq
Begin (* 1 *) ?
End (* 1308
*) ?
Is this sequence circular (* No *) ?
Enzyme(* * *):
What should I call the output file (* Platelet.Mapsort *) ?
Type the file Platelet.mapsort to see the list of fragments and the (numbered) cut-sites. At the bottom of the file enzymes are classified as "DO CUT", "DO NOT CUT" and "EXCLUDED" with the exclusion criteria described.
All previous examples showed how to select from the entire list of enzymes. You can select directly by name, eg: using MAPSORT to perform a complete digest.
$ Mapsort/digest
(Linear) (Digest) MAPSORT of what sequence ? platelet.seq
Begin (* 1 *) ?
End (* 1308 *) ?
Is this sequence circular (* No *) ?
Enzyme (* * *): TaqI
"TAQI" selected 1 enzyme, new total: 1 Enzyme: AluI .
"ALUI" selected 1 enzyme, new total: 2 Enzyme: Mae* .
"MAE*" selected 3 enzymes, new total: 5 Enzyme:
What should I call the output file (* Platelet.mapsort *)
Type the file Platelet.mapsort. The /digest command shows the fragments obtained when all enzymes are used simultaneously, in place of the fragments obtained for each enzyme.
MAPSORT/plasmid produces an output file suitable for PLASMIDMAP. This example identifies all enzyme sites unique to the non coding region.
$ Mapsort/exclude=388,1020/plasmid
(Circular) MAPSORT of what sequence? Platelet.seq
Begin (* 1 *) ?
End (* 1308 *) ?
Enzyme (* * *):
What should I call the output file (* Platelet.tick *)
$ Plasmidmap/font=1 platelet.tick
{accept all the defaults}
PLASMIDMAP command line options are common to many other graphics-display programs.
Identify all the sixbase enzyme sites unique to WITHIN the coding region by using the /exclude option to exclude both non-coding regions, then label the diagram.
$ Mapsort/exclude=1,387,1021,1308/six/plasmid
$ Plasmidmap/font=1/title="Coding region sites" platelet.tick
To obtain a copy of the data file which contains the full set of enzymes and definitions of cut sites:
$ FETCH enzyme.dat
If this file is in your default directory, the mapping programs will use that file. (See chapter 2-6 on local data files). The files ENZ_REFS.TXT (published references for the enzymes) and ENZ_SOURCES.TXT (addresses of suppliers) can also be fetched.
The program PEPTIDEMAP works exactly like the program MAP, offering a list of proteolytic enzymes and reagents. PEPTIDESORT shows the peptides obtained from a digest of a larger peptide and the molecular weight of the starting protein.