Restriction enzyme digest of
complete genomes and Pulsed Field Gel
Electrophoresis (PFGE)
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.
Example
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Sequence:
Restriction enzyme:
Recognition sequence:
Cleavage positions:
Cleavage positions recorded:
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5'-GGGCCC-3'
AspS9I
G'GNC_C
1 and 2
1 |
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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