Primers database through gopher.

Michael Finney finney at Frodo.MGH.Harvard.EDU
Tue Sep 21 20:56:46 EST 1993

Thanks for taking the time to organize this database.  The form looks fairly 
good, i.e., has most of the information one would want.  

There seems to be some confusion as to whether this is a database of *primers* 
or of *primer pairs*.  Either one would be OK, but y'all need to make up your 
minds.  If it is a database of primers, then product lengths need to be given 
for *each* matching primer; as written it is not clear which pair the sizes 
are given for.  If it is a database of pairs, then names and sequences of both 
primers need to be given.

Many people use degenerate primers to clone homologs of known genes.  There 
needs to be a guide for entering degenerate sequences.  The species line would 
then need to indicate the group for which the primers are likely to work 
(e.g., "vertebrates" or "eukaryotes").

It is not exactly clear to me what one would put in the "flanking bases" line.  
Does this mean the beginning and end of the product?  With what matching 
primer?  Including the primer sequence or not?  And using what sequence 
numbering system?  An accession number would be ideal, but failing that, the 
numbering should be from some explicit reference point (different for each 
gene; perhaps the AUG or the 5'-most transcription start site).

Since many primers contain sequence alterations, some description is needed of 
which bases are complementary to the target.

A nice feature would be to have the database site do a TM calculation (both 
for the whole primer and the target-complementary region?).  This would 
guarantee that all TM estimates in the database would be done the same way, so 
that users could compare apples to apples.

Under Cycling Conditions, it is important to know amount, source, and type of 
target DNA; conditions for amplifying from 1 ng of a clone are different than 
for amplifying from 1 ng genomic DNA.

Under Buffer Constituents, it might be good to list standard conditions and 
ask people to note any differences.  This saves time, and doesn't assume 
everyone knows what the standard buffer is.

Mike Finney

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