Its value is the minimum number of basepairs in the enzyme recognition sequence, adjusted for ambiguity. Back to section 1. However, we will visit the faster site hosted by the creator of the webcutter tool. The web cutter home page will appear, containing a number of text fields that allow you to tailor your restriction analysis. Sets the color used to highlight sites that appear only once in the sequence.

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Amino acids allowed at the beginning of an open reading frame. All enzyme names in the Enzyme Picker are hyperlinked to explanation windows.

Requires open reading frames to have a minimum length. The save button stores the present values of the form.

If a protein sequence is entered, a map will be displayed showing all possible restriction sites allowed by back-translation of the sequence. 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.

Allows qebcutter to overlap by this number of basepairs without causing rejection. A blank means any residue is acceptable. If set to Yes, restriction sites that are predicted not to be cleaved because of overlapping E.

Yes No Enzyme Choices Identifies enzymes that will be added to the map, overriding other controls. Can be used to provide a local file containing data on the enzymes to be used. In addition to cut and paste, you can upload the sequence from your computer on floppy or Hard disk or you can retrieve them directly from the GenBank database.

Whatever is entered will be repeated throughout the sequence. Enzymes added to webcjtter map by default as specified by the Site Complexity field are highlighted in the Enzyme Picker. There are a number of options you can change simply by clicking the appropriate option buttons below the sequence entry box. The reset button restores the page defaults without changing the stored preferences.

Integer values are not required. Used to reject enzymes that cut too frequently.

WebCutter 2.0 - A restriction mapping tool

Sets the font color of the translated sequence names. 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. Its value is the minimum number of basepairs in the enzyme recognition sequence, adjusted for ambiguity.

The entire browser window i. Also sets the font color for the end fragments of linear sequences, which may not correspond to physical fragments. Sets the color of the amino acid links. Click here to launch Web cutter. Enzymes that are commonly used for cloning are highlighted in colour — e. Back to section 1. To display only specific enzymes, set the minimum complexity to some large number and then choose the desired enzymes from the picker.

Any red green blue hexadecimal code of the form rrggbb, e. You will be presented with a graphical representation of you sequence with the restriction sites printed alongside the sequence and a table that lists the position of the target sequences in your sequence.

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Creates a custom separator between the top and bottom lines of the displayed sequence. Sets the font color of the enzymes that cut three or more times in the sequence. One common task in the analysis of nucleotide sequences is that of searching for restriction sites.

Sets the color of the enzymes selected with the enzyme picker or entered directly in the Enzyme Choices text box.

Removes any saved preferences without changing the values entered in the form.

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