Primers database through gopher

Luc Simon lsimon at
Tue Sep 21 14:05:26 EST 1993

In article <1993Sep20.173632.24356 at>, pc386 at
(BENNY SHOMER 9238) wrote:

> Hello Bionetters.
> It has been recently suggested that a searchable database of primers 
> for PCR will be set. The basic idea behind this database is that only
> ___TESTED_&_WORKING___ (!!!) primers should be contained. This may save
> many valuable planning and working hours, as well as money. We all know
> that even carefully planned primers fail to operate when it comes down
> to the tubes...  
> Dan Jacobson from the Johns Hopkins Univ. GDB, and your humble servant, are
> now working on the establishment of this database as a gopher server. 
> Cited below is the suggested basic form for this database. We now open a 
> discussion regarding the suggested data fields. We are interested in hearing
> your opinions regarding this form. 

Many kudos to Dan and Benny for actually setting up a service that promises
to be invaluable in the very near future!

Here are a few suggestions: 

Since this database will be accessed tru Gopher, and probably Wais-indexed
so that a simple query should be replied by a number of pertinent records,
why not make each record contain all the information pertaining to a given
PCR assay. In other words, make it a database of PCR assays instead of a
database of PCR primers. This would really only translate in adding all
information about the "matching primer" to the proposed form. This way, the
user of the database will not need to parse a possibly large number of
records to pair matching primers manually. The database would also be more
compact since information such as product lenght and cycle conditions need
not be repeated twice. An important benefit of that approach is that Primer
Names do not need to be unique, as is implied in the suggested form where
the user is expected to be able to fetch the matching primer only knowing
its name.

I suggest that enough space is allowed in the Species field to allow proper
description of "multi-purpose assays", using degenerate primers or primers
derived from conserved genes that could be useful on a variety of

I also suggest to move the reference field from the "submitting author"
part of the form to the "PCR assay" part of the form.

In the cycle conditions, the type (make and model) of thermocycler used
might be specified.


Luc Simon

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