PCR primers and hybridization probes

[Bruce Roe]

In article <1993Sep13.184334.25805 at cas.org>, ljc55 at cas.org writes...
> 
> 
>	  For those of you interested in PCR primers and hybridization
>      probes I would really appreciate your opinions about their
>      inclusion in biosequence databases.  Some of my specific concerns
>      are as follows:
> 
>      1.  Do you feel primers and probes tend to clutter up a nucleic acid
>	  database and cause unnecessary retrievals when searching for
>	  sequences of much longer length?

Linda,
	I really don't see there is a problem with getting many "hits"
on primers and hybridization probes when searching the GenBank databases.
Actually it would be nice to get some "hits" as that would give us people
to contact to find more information about an unknown gene we've just
sequenced.

> 
>      2.  Because primers and probes are usually designed from known sequence
>	  information often already in the database, is it still justifiable
>	  to include them as additional entries?

Because your address indicates you are with CAS, are you thinking of
adding them to CAS?

> 
>      3.  What applications of primers and probes should justify their
>	  inclusion in a biosequence database, e.g.  clinical diagnosis,
>	  taxonomy, evolution, gene mapping, or methods?

Information regarding primers and probes IS included in the Genome Database
at John's Hopkins (GDB) and is very useful for folks doing clinical diagnosis,
taxonomy, evolution, and gene mapping.
> 
>     4.   If you were to search for primers and probes in a biosequence
>	  database what would be most efficient for you?  Would some type of
>	  descriptive information be helpful, e.g. their application or
>	  their origin?

Yes, and this information already is available, on-line, for FREE, at GDB.

> 
> 
>	  Thank you very much for any thoughts you might have on this subject.
> 
>	  Please post your response to ljc55 at cas.org

Another poster flamed you on this one.  You might want to read some of
the stuff that get's posted or search the biosci archives before posting
and then requesting the responses be sent to you.  Proper Net Etiquete (sp)
would be to say:

	Please post your response to ljc55 at cas.org and I will post a
 SUMMARY of responses.

Cheers and this post to you was meant NOT to be a flame.
--bruce
  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 \  Bruce A. Roe                 Professor of Chemistry and Biochemistry /
 /  Dept. of Chem. and Biochem.  INTERNET: BROE at aardvark.ucs.uoknor.edu  \
 \  University of Oklahoma       BITNET:   BROE at uokucsvx                 /
 /  620 Parrington Oval, Rm 208  AT&TNET:  405-325-4912 or 405-325-7610  \
 \  Norman, Oklahoma 73019       FAXnet:   405-325-6111                  /
  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  - - -