Restriction enzyme digest of complete genomes and Pulsed Field Gel Electrophoresis (PFGE)

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All commercially available restriction enzymes were used to compute the number of times the corresponding sequence was present in the genome. These calculations were originally obtained to allow easy selection of endonucleases for PFGE.

Chromosomes were considered circular (unless they were linear) and plasmids were considered always circular.

In the calculations shown in this pages, we only recorded the first cut generated by overlapped recognition sequences. The number of fragments generated by a sequence which shows overlapping will not change the band pattern in a PFGE experiment (the sensitivity of PFGE will not allow to discern such a small diferences in the length of fragments). But this fact may be importante in other techniques. When overlapping happened only the first matching recognition sequence (starting in 5' end) was recorded.


  Restriction enzyme:
  Recognition sequence:
  Cleavage positions:
  Cleavage positions recorded:  
1 and 2

A list of all restriction enzyme specificities and corresponding numbers of theoretical cleavage positions was obtained. All this data was included in a database, searchable by number of cleavages (between minimum and maximum) and type of restriction enzyme. Number of cleavages for specific endonucleases may be also requested by selecting them.

When the number of cleavages for a specific restriction enzyme was 50 or smaller
, cleavage positions and length of fragment obtained were calculated. This data is available by clicking on number of fragments. The resulting page will show the positions where the genome is cleaved, and the length of the resulting DNA fragment. In a third column, sorted lengths of fragments are shown, and a simulation of a Pulsed Field Gel Electrophoresis in 1.2% agarose (PFGE) with Molecular Weight Markers (Lambda ladder), it is also shown.

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