DNA 5
Site Complexity:
Used to reject enzymes that cut too frequently. Its value is the minimum number of basepairs in the enzyme recognition sequence, adjusted for ambiguity. For example, if the minimum is set to 6, enzymes that recognize unambiguous sequences less than 6 basepairs long, or that recognize a 6 basepair sequence with at least one ambiguous basepair, will not be included in the map. Integer values are not required.
≥
Residues
Reject coli methyl:
If set to Yes, restriction sites that are predicted not to be cleaved because of overlapping
E. coli dcm
or
dam
methylation will not be included in the map or fragment list. Cleavage site resistance information is based on the enzyme providers' descriptions.
Yes
No
Enzyme Choices
Identifies enzymes that will be added to the map, overriding other controls. The names of the enzymes specified here will be given a distinct color (and/or appearance), as specified by the Selected Enzymes switch. Enzymes added to the map by default (as specified by the Site Complexity field) are highlighted in the Enzyme Picker. All enzyme names in the Enzyme Picker are hyperlinked to explanation windows. Checking a highlighted enzyme will change its color in the map. To display only specific enzymes, set the minimum complexity to some large number and then choose the desired enzymes from the picker. Enzymes can also be added to the text field directly.
Enzyme File:
Can be used to provide a local file containing data on the enzymes to be used. The file must have the same structure as the file "enzymeData" in subfolder /enz/ of this site.
Start Residues:
Amino acids allowed at the beginning of an open reading frame. A blank means any residue is acceptable. A choice to capture additional bacterial orfs might be MVIL.
Reject Overlapping Orfs:
Allows or prevents the display of overlapping open reading frames. Usually the longest open reading frame will exclude all smaller overlapping orfs but improbable long orfs (e.g. containing homopolymers) can also be rejected.
Yes
No
Frames Wanted
These checkboxes allow various reading frames to be shown. The application does not attempt to identify open reading frames in ENA/DDBJ/GenBank pages unless the Tags/Extra Orfs checkbox at the right top of the sequence box is checked.
1
2
3
for
all
orf
-1
-2
-3
rev
no
gb+
Allowed Overlap:
Allows orfs to overlap by this number of basepairs without causing rejection.
Minimum Orf Length:
Requires open reading frames to have a minimum length. Blank = 0.
Basepairs
Basepairs
Sequence Width:
Sets the number of basepairs displayed per line.
Characters Per Line
Separator Template:
Creates a custom separator between the top and bottom lines of the displayed sequence. Whatever is entered will be repeated throughout the sequence.
Page Background
Sets the background color of the page.
Unique Sites:
Sets the color used to highlight sites that appear only once in the sequence. Any red green blue hexadecimal code of the form #rrggbb, e.g. #9a80ff, can be entered (the hexadecimal digits are 0-9a-f).
Amino Acids:
Sets the color of the amino acid links. Any red green blue hexadecimal code of the form #rrggbb, e.g. #9a80ff, can be entered (the hexadecimal digits are 0-9a-f).
Variation Highlight:
Sets the highlight color (background color) of any sequence variation sites listed in the sequence feature table if the Show Variations switch is set to Yes.
Selected Enzymes:
Sets the color of the enzymes selected with the enzyme picker (or entered directly in the Enzyme Choices text box).
Translations:
Sets the font color of the translated sequence names. Also sets the font color for the end fragments of linear sequences, which may not correspond to physical fragments.
Sequence:
Sets the color of the sequence itself.
Enzymes:
Sets the font color of the enzymes that cut three or more times in the sequence.
Preferences:
The save button stores the present values of the form. The reset button restores the page defaults without changing the stored preferences.
Cookie:
Removes any saved preferences without changing the values entered in the form.
Circular
Linear
Default
Tags/Extra Orfs
Filter
Paste Your Sequence or GenBank Page Here
Supported Formats
The supported formats include DDBJ, ENA, GCG, GenBank, FASTA and plain text. The entire browser window (i.e., the result of a "select all") for a GenBank/ENA/DDBJ page can be pasted into the text box. Tags/Extra Orfs finds and adds orfs independent of the archive feature annotation. If a protein sequence is entered, a map will be displayed showing all possible restriction sites allowed by back-translation of the sequence.
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