RestrictionMapper FAQ

How do I use RestrictionMapper?

Check out the help page.

How does RestrictionMapper work?

It's a Perl script that accesses a MySQL database of restriction enzymes. The database was populated from a REBASE file (format 19), using another Perl script.

What's the point of putting restriction mapping on the Web? There's plenty of stand alone software that does this.

Web based software can be updated as new restriction enzymes are made available, saving the user the trouble. RestrictionMapper also provides a convenient link to the REBASE information for each enzyme in your output table. Plus, you can't beat the price.

Why doesn't RestrictionMapper include non-commercial enzymes?

Because they're not worth the trouble. There are about 3,000 known restriction endonucleases and fewer than 600 are available commercially. Your output table would be five times as long and about 80% of the enzymes on it would be unavailable.

Why does RestrictionMapper show the same sites in slightly different locations than some other restriction mapping software?

RestrictionMapper reports actual cutpoints, as opposed to just the first nucleotide in the recognition sequence.

RestrictionMapper didn't report a site that I know is in my sequence. Why?

Some enzymes have cutpoints that are offset from their recognition sequences. If either the input strand cutpoint or the complementary strand cutpoint is off the end of a linear sequence, the enzyme won't digest at that site and RestrictionMapper won't report it. Or, the enzyme might be non-commercial or excluded by your selection criteria.

RestrictionMapper reported a site that I can't find in my sequence. Why?

If the recognition site is not palindromic, look for the reverse complement of the site.

Who do I contact to report a bug in RestrictionMapper?

Email me, Peter Blaiklock, at peter.blaiklock |AT|

Will RestrictionMapper be upgraded in the future?

Yes, although there is no timetable. Coming improvements may include:

  1. A reverse complementation function.
  2. The ability to find and translate open reading frames.
  3. The ability to draw a graphical map of a sequence.

Please email me any suggestions at the above address.

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