SGD Help: Yeast Genome Restriction Analysis
The Yeast Genome Restriction Analysis software, accessible from the "Analyze" section of the menu bar, can be used to generate a restriction map of a given DNA sequence. Either the name of the sequence (gene name, ORF name, GenBank name, or clone name) or an actual DNA sequence can be entered. 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. The Yeast Genome Restriction Analysis tool includes a non-redundant set of enzymes. If a restriction enzyme that cuts a specific site is known by 3 different names (aka, isoschizomers), only 1 name will be included in the analysis. In order to identify if a restriction enzyme is known by another name, you can search the Restriction Enzyme Database.
Contents
- Using the Yeast Genome Restriction Analysis Tool
- Results Display
Using the Yeast Genome Restriction Analysis tool
- Step 1: Enter a sequence name or a DNA sequence
- a. Enter a sequence name With this input option, you can enter a gene name, an ORF name, a GenBank sequence name or accession number, or an ATCC clone name. Note that you can also enter the first few characters of a sequence name, followed by an asterisk; you will then 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).
- b. Enter a DNA 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.
- Step 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.
- Step 3: Click the "Display Map" button
Results Display
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 left side of the graphic. 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. Placing your mouse over the restriction map or name of an enzyme will provide a tooltip with information about the enzyme, including its recognition sequence, a size-sorted list of the first 10 fragments that would be generated if the input sequence were digested with that enzyme only, and the exact coordinates of first 10 sites on each strand where the enzyme cuts the input sequence. For a complete list of enzyme restriction fragments and cut sites, click the "Download Restriction Site Results" link.
The enzymes that do not cut the sequence are listed in alphabetical order below the main display. Click the "Download 'Do Not Cut' Enzyme List" link near the top of the main display to generate a text file listing all these enzymes.