AspGD Help: AspGD Restriction Analysis


Contents



Description

The AspGD Restriction Analysis software can be used to generate a restriction map of a given DNA sequence. Either the name of the sequence (gene name, ORF name) can be given or an actual DNA sequence. The user can choose whether the restriction map shows all enzymes, enzymes that generate 3' overhangs, 5' overhangs, or blunt ends, or enzymes that cut once or twice.

Using the AspGD Restriction Analysis tool

  1. Select or enter a sequence

    1. Enter a gene name and select a species

      With this input option, you can enter a gene name, or an ORF name. Note that you can also enter the first few characters of a sequence name, followed by an asterisk: you will be presented with a list of possible completions from which you can select a single sequence (click on the "Reset form" button if you want to delete your current entry and enter a new one). Select a species from the pull-down menu.

    2. Enter a sequence

      With this input option, you can type or paste a DNA sequence. Only the four letters, "A", "G", "C", and "T" should be entered (although numbers are allowed). Any other text will be interpreted as not matching the enzyme recognition sequences, although no error message will be given.

  2. Choose the category of enzymes

    Six different restriction maps can be generated, depending on the category of enzymes chosen: all enzymes; enzymes that generate 3' overhangs, 5' overhangs, or blunt ends; or enzymes that cut once or twice. The category can be chosen from the pull-down menu. To get a list of the enzymes that do not cut the given sequence, choose "all" enzymes: the output page will also list at the bottom of the page those enzymes that do not cut.

  3. Click the "Display Map" button

    The output display consists of a single line, representing the input sequence (along with coordinate numbers), and a line for each enzyme (within the chosen category) that cuts the sequence. The location of a recognition site is shown with a red or blue tick mark. A red tick mark indicates where the recognition sequence was found in the Watson (5'-->3') strand, while a blue tick mark indicates where the recognition sequence was found in the Crick (3'-->5') strand.

    The enzymes (within the chosen category) that cut the sequence are listed in alphabetical order on the right side of the graphic. Clicking on the name of an enzyme will provide further information about the enzyme, including its recognition sequence, the exact coordinates of where the enzyme cuts the input sequence, and a size-sorted list of the fragments that would be generated if the input sequence were digested with that enzyme only. Enzymes that generate 3' overhangs are displayed with a green name, while magenta and orange are used for enzymes that generate 5' overhangs and blunt ends, respectively.

    The enzymes that do not cut the sequence are listed in alphabetical order below the main display.

    The output display may be split over more than one page if many enzymes cut the input sequence, in which case clicking on the link labeled "View next page of Restriction Map, enzyme..." or "View previous page of Restriction Map, enzyme..." will bring up the other page of display.

Restriction Enzymes Included

The tool includes a non-redundant set of enzymes. If a restriction enzyme has several isoschizomers, only one enzyme that cuts each site will be included in the analysis. In order to identify isoschizomers, you can search the Restriction Enzyme Database at New England Biolabs.

Accessing the AspGD Restriction Analysis tool

The AspGD Restriction Analysis page can be accessed by selecting the "Restriction Analysis" link on the Search Options contents page

Other Relevant Links

  1. Gene/Sequence Resources at AspGD, where can be found alternative restriction digest software provided by GCG.
  2. Restriction Enzyme Database, for identifying isoschizomers
Go to Aspergillus Genome Restriction Analysis


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