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The Find restriction sites dialog appears:
The tree of restriction enzymes
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- Suppliers - check/uncheck suppliers, whose enzymes will be shown. By default, enzymes with undefined commercial suppliers are not shown.
- Recognition sequence length - show only enzymes, whose recognition sequence length is in bounds. NOTE: N bases are not included in recognition site. That means, that if enzyme has the following sequence:
C C N N N N N N N G G
its recognition site length will be four, not eleven. - Overhang type - show only enzymes with certain overhang type. The following options are presented:
- Any - show all enzymes.
- No overhang - site has no cuts at all. Example:
3' CTCGAG 5'
5' GAGCTC 3' - 5' - the cut of the forward strand is to the left of the cut of the reverse-complementary strand. Example:
3' C C▼T N A G G 5'
5' G G A N T▲C C 3' - 3' - the cut of the forward strand is to the right of the cut of the reverse-complementary strand. Example:
3' C G A T▼C G 5'
5' G C▲T A G C 3' - Blunt - the cut is cuts are located in the middle of the site.
- Sticky - the cut is cuts are locate anywhere but the middle of the site. It is 5' and 3' both.
- Nondegenerate sticky - the same as Sticky, but the overhang between cuts has only A, C, G or T (no extended) symbols.
- Blunt or sticky - Blunt + Sticky.
- Blunt or nondegenerate sticky - Blunt + Nondegenerate sticky.
- Keep only - show most interesting enzymes only:
- Palindromic - forward and reverse-complementary strands are equal.
- Uninterrupted - no internal N bases.
- Nondegenerate - No no extended DNA alphabet symbols (only A, C, G, T and N).
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The region to search enzymes in. You may also Exclude some region and not to search in itIf you check the Uncut area checkbox,.than restriction enzymes, which exists outside of the uncut area, but also presisted inside of it, won't be included in the result.
Example:
You will find two "AsaI" enzymes in the following sequence if you choose the whole sequence as Search in:
But, if you also set Uncut area to 60-90 you will not find enzymes at all and will see the following sing in the log: The following enzymes were found, but skipped because they are presented inside of the "Uncut area": Aasi.
The information about enzymes was obtained from the REBASE database. For each enzyme in the list a brief description is available (the accession ID in the database, the recognition sequence, etc.). If you’re online you can get more detailed information about an enzyme selected by clicking the REBASE Info button.
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