Webgenetics: Ristriction Enzyme Analysis

This program does digest analysis with restriction enzymes of DNA sequences (run the other program to get information about restriction enzymes such as commercial availability, methylation, references). The sequence can be both in upper case or lower case, and non-alphabetic characters are ignored. The program uses rebase of NAR format. The name of an enzyme must not contain spaces in it. For example, EcoRI must be given as EcoRI or ecori, but NOT EcoR I. Case is not important. Make sure you do not substitute Roman numbers with Arabic digits. For example, EcoRI must not be given as EcoR1. In cases of unrecognized enzymes, either check your spelling or notify help@webgenetics.com.

Example outputs:

Example1:

mp18: 7250 bps

      Enzymes  Sequences   Sites  Fragments  Sorted

  1.    BanII    gggctc     5645     6646     6646
  2.     AvaI    ctcggg     5827      182      406
  3.    EcoRI    gaattc     6233      406      182
  4.    BanII    gagctc     6239        6       10
  5.     AvaI    cccggg     6249       10        6

        Following enzymes cut only once:
               EcoRI

The sequences are sequences recoganized by the cutting enzymes. The sites refer to the bases before the cutting sites for blunt cuts, or refer to the bases at the middle for staggered cuts. The last two columns are sizes of fragments generated by the digestion, in order of cut sites and fragment sizes respectively. They are calculated based on the sites of cuts.

Example2:
                  mp18 (7250 bps) digested with DraI

size scale        7360      3680      1840       920       460       230
                    .         .         .         .         .         .         

               mp18         |         |                        |   2

This gives an estimated gel pattern of the fragments of digestion based on the assumption that the migration rate of a fragment is reciprocally proportional to log2(size) (not accurate but common practice). A number indicates the number of bands at that position. A letter N indicates more than 9 bands at that position.

Example3:

     mp18: 7250 bps. Each dash is about 120 bps
  AacI         1 ---------------------------------------------------1--------
  AaeI         1 ---------------------------------------------------1--------
  AagI         2 --------------------1-----------------------------------1---
  AaqI         1 ---------------------------------------1--------------------
* AauI         1 --------1---------------------------------------------------
  AcaII        1 ---------------------------------------------------1--------
  AcaIII       1 -----------------------------------------------------1------
  AcaIV       15 -----------1------1--1--------------------112--1-2--21-1--1-
* Acc16I       1 -----------------------------------------------------1------
  Acc38I       7 --------1-------1--------------------------------21-11------
* Acc65I       1 ---------------------------------------------------1--------
...

This shows digestion maps of all enzymes in the database. Enzymes marked with asterisks are commercially available (at the time the database was compiled). The number at left of each dash line is the total number of cuts. The numbers within the dash lines indicate the number of cuts in the region of a dash length and a N indicates more than 9 cuts..

Restriction Enzyme Analysis of DNA Sequences