University of Helsinki

Database format

Restriction Enzymes database format

N> name of the enzyme
S>recognition site of the enzyme. The / represents the cutting position
M> dam or dcm methylation sensitivity of the enzyme - 1 for sensitive, 0 for not
T> optimal digestion temperature of the enzyme
B> digestion buffer of the enzyme by company
Note: the last two fields are not currently used by PlasmaDNA but are included for possible future features in the program.

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NOTE: As of version 1.4, the restriction enzyme databe used is the gtype2c.XXX format from REBase, from where updated versions can be downloaded. The Enzymes.pdat file contains instead the names of the enzymes present in your laboratory.

 

Primers database format

(name of primer) SPACE (5'non-annealing sequence) SPACE (annealing sequence) END OF LINE

Note: if a primer does not contain a 5' non-annealing sequence, please use "X" as a place holder

The name of primer can not contain spaces

Domains database format

 

$ beginning of file mark - important!

T> Type of domain. This will determine the color on the graphical drawing of the fragment.

N> Name of the domain as it will appear on the graphical drawing of the fragment

S> Sequence of the domain. This is the sequence that PlasmaDNA will look for in all new sequences entered in the program. It can NOT contain degenerated (N) bases.

D> Description of domain as it will appear in the domain information sub-window.

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