DNA 5


Site Complexity:This field is 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 this switch is 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 ChoicesThis field 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:This button 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 "enzyme data" in subfolder /enz/ of this site.
Start Residues:This field can be filled with letters representing the acceptable amino acids for the beginning of an open reading frame. A blank signifies any amino acid is acceptable. A common string for bacterial genes might be MVIL. Reject Overlapping Orfs:This switch allows or prevents the display of overlapping open reading frames from input sequences that do not conform to GenBank format. If set to Yes the longest open reading frame for any given region will exclude all smaller overlapping orfs. Yes No
Frames WantedThese checkboxes allow the predicted translations of the sequence to be included. By default the application does not attempt to identify open reading frames in GenBank pages, but defers to the translations identified in the GenBank page Features field. Otherwise the algorithm used to identify orfs consists of translating all frames and identifying the longest run of sequences that begin with an acceptable amino acid and end with a stop codon (this does not take initiation codon context into account). If overlapping open reading frames are not desired (the default in the corresponding preference switch) the orfs are then sorted by length and any that overlap with the longest are removed. The longest surviving orf is then chosen from the remaining list and the procedure repeated until no candidate orfs remain to be tested.
1 2 3 for all orf
-1 -2 -3 rev no gb+
Minimum Orf Length:This field prevents the display of potential open reading frames having a length less than the specified number of basepairs. Basepairs
Sequence Width:This field sets the number of basepairs displayed per line. Characters Per Line Separator Template:This field can be used to override the default separator between the top and bottom lines of the displayed sequence. Whatever string is entered will be repeated throughout the sequence.
Page BackgroundThis field sets the background color of the map.
Unique Sites:This field 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:This field 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:This field 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:This field sets the color of the enzymes selected with the enzyme picker (or entered directly in the Enzyme Choices text box).
Translations:This field sets the font color of the translated sequence names. It also sets the font color for the end fragments of linear sequences, which may not correspond to physical fragments.
Sequence:This field sets the color of the sequence itself.
Enzymes:This field sets the font color of the enzymes that cut three or more times in the sequence.
Preferences:The save button allows the present values of the form to be stored. The reset button restores the page defaults without changing the stored preferences.
Cookie:This button causes the preferences cookie to be removed from your browser-specified cookie file, which will remove any saved preferences without changing the values entered in the form. This may be useful if the preferences form has changed since you last visited the site.
Circular Linear Default Tags/Extra Orfs
Supported FormatsThe supported formats include GenBank, ENA, DDBJ, GCG, FASTA and raw sequence. 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 GenBank/ENA/DDBJ 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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