Primers database through gopher.

BENNY SHOMER 9238 pc386 at ccsg.tau.ac.il
Mon Sep 20 12:37:42 EST 1993


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. 
Please pay attention to the following:
1. This message has been cross posted to several bionet.xxxx groups. It is 
suggested however, that the thread will be maintained in bionet.molbio.   
methds-reagnts . This will make it easier to read and respond to everyone's
followups.
2. A followup to the newsgroup is prefferred over direct responses in the 
Email, so as to keep the thread open. If, for any reason you want to contact
us directly, Dan's address is: danj at gdb.org, my @ is: pc386 at ccsg.tau.ac.il

We hope that this thread will be constructive, and that the database will be
'on the air' as soon as possible.

Greetings,
Dan Jacobson,
Benny Shomer.

     
                           This is the suggested form:

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Primer Name: ______________________________

Target Gene: ______________________________________________________________

Species: ___________________________   

Direction: { FOR / REV } 

Matching Primer(s) in this database: _________________________________

Sequence (5' --> 3'): ___________________________     
Length: __
Flanking bases ______ to _____ on the target sequence. 

Product Length (cDNA):_______ 
Product Length (genomic):_______ 

{Lengths are in bp, or 0 for inverse PCR, where length is unknown}

Restriction Site Added: _____________   

Mutation presented at base: __ 

Special Applications: { Inverse/ RT-PCR/ Sequencing/ Cloning/ Mutation/
                         / Ligation Mediated} 

__________________________________________________________________________

__________________________________________________________________________

********************    Cycle Conditions *********************************

Hot Start: {Yes/No}

Initial Denaturation-  Temp: __      
                       Time: ____

Denaturation -  Temp: __      
                Time: ____

Annealing -     Temp: __      
                Time: ____

Extension -     Temp: __      
                Time: ____

Number Of Cycles: __ 

Final Extension -     Temp: __      
                      Time: ____



**********************   Buffer Constituents  ****************************

(This section basically regards non-standard buffer constituents)

Reaction Volume (ul): __

Used Standard Buffer Supplied By: _______________


MgCl2 Concentration (mM): __      
DMSO Concentration (%): __ 

Formamide Concentration (%): __   
Gelatin Concentration (%): __ 

dNTP's Concentration (uM): __     
Primers Concentration (uM): __ 

Polymerase Type: ___________   
Polymerase Concentration (U/Rxn.): ___ 

Make: _____________

**************************************************************************

Submitting Author.

Name: __________________________________

Institution: ______________________________________________________________

__________________________________________________________________________

Address: _________________________________________________________________

__________________________________________________________________________

E-mail : ________________________________    
Fax# : ______________________

References:

__________________________________________________________________________

__________________________________________________________________________

__________________________________________________________________________

Remarks:

__________________________________________________________________________

__________________________________________________________________________

__________________________________________________________________________

__________________________________________________________________________

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



 **************************************************************
* Benny Shomer                                                 *
* Tel-Aviv University                                          *
* Sackler School of Medicine, Dept.of Embryology and Teratology*
*--------------------------------------------------------------*
* Snail:  Ramat-Aviv , Tel-Aviv  69978 ,  Israel.              *
* E-mail :  pc386 at ccsg.tau.ac.il                               *
* Tel :  972-3-640-9238     FAX :   972-3-642-2046             *
*                                                              *
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