RFLP enzyme picker

Purpose of this page

This web page is designed to find restriction enzymes that cut one variant but no the other of a polymorphic site. The program looks for restriction sites that contain the variant base (identified by the use of an IUPAC 1-letter code abbreviation) in the input sequence. Where a restriction site is cleaved by more than one enzyme, the names are place on the same line, occasional this may extend beyond the visible part of the textbox. In these cases use the horizontal scrollbar to see the full list. Where the enzyme name is followed by a '(F)', it indicates that the enzyme cuts the DNA in the flanking sequence and not in the enzymes binding site. If 'Check -' is on the same line it indicates that the recognition consensus sequence contains positions that can be three (B, D, H or V) or four (N) of the four nucleotides. These may confuse the program and so you should check that the enzyme is suitable. If an enzyme also cuts other sites in the sequence these sites are shown below the sequence. Enzymes that have a non-palindromic site are screened against the test sequence in both directions and may appear twice in the results.

The web page also looks for overlapping restriction sites ofdegenerate sites. e.g. try this sequence: agaaggactgactctStatcgcgagagcggagctccaagcccggcag.  This fragment has two overlapping sites for the non-palindromic Hin4I enzyme, one site contains the S base while the other does not.

A Windows program that duplicates this page can be downloaded here.

Instructions

Enter the sequence around the variant base (maximum length of 50bp). The variant base should be identified using a degenerate nucleotide letter.
(Test sequence = acgtgcaccgtcatgacgacgaaYtcgcatgatcgactgactg note the polymorphic 'Y' residue, if you change the 'Y' for a 'S' the selected enzymes change.)

Press the button to analysis the variant