StrainMan 1.0 Question

Robert Negm rnegm at med-med1.bu.edu
Thu Jun 4 14:04:23 EST 1998


To whom it may concern,

I am writing to answer a common question regarding StrainMan 1.0 from
Caesar Software at http://www.caesarsoftware.com.

The highly asked question I have been receiving is, "How can I use
StrainMan to find the strains in my collection that harbor plasmids,
which also contain a unique restriction site?"


The answer is the following. Create a new plasmid or edit one currently
in the plasmid list by first, selecting the "Plasmid" tab in the main
list and then pressing the "New" or "Edit" button. Once you have opened
the plasmid record click on the "Genetics" tab. Click on the "Sequence"
button. Here you may paste the sequence of DNA into the large field.
After you paste the DNA sequence of the plasmid into a text field, press

the "OK" button. Then press the digest button, and StrainMan will scan
this strand and its complement  for restriction site motifs.  Save the
new or modified plasmid record. Select a strain from your collection by
clicking on the "Strain" tab in the main list and clicking on a strain
in the collection. Once the strain record is open, then select the
"Plasmid & Phage" and press the "Attach" button to the right of the
plasmid list. Now click on the plasmid that you recently entered into
the StrainMan database that contains its  restriction map and press the
"Select" button. Press the "Save" button on the strain record.

Now you may search for this strain by using the search engine from
"Search" pull-down menu and select "Search". Select the "Plasmid: enzyme

name", and enter in the restriction enzyme name into the right field.
Press the "More Choices" button then select the "Plasmid: # cut sites",
then enter "1" into the field on the right. Press the "Find" button and
StrainMan will retrieve all strains in your collection meeting the this
criteria.

Remember, if there are rare enzymes not already present in StrainMan,
then users must enter the enzyme name and motif into the enzyme list. To

do this select "Enzymes" from the "Utilities" pull-down menu, enter the
enzyme abbreviated name and motif. Look at other enzymes by clicking on
them to see how to annotate the exact restriction site by placing a
quotation mark and a comma between the one-letter nucleotide
abbreviations for top and bottom strands, respectively.

As always, all of this information is present in the users manual and
the on-line help. If you have any more questions, then please feel free
to contact me directly.


Sincerely,

Robert Negm, PhD
Scientific Advisor
Caesar Software LLC
http://www.caesarsoftware.com









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