PCR Primers Database - Submission form.

Benny Shomer bshomer at ebi.ac.uk
Fri Nov 10 06:06:19 EST 1995


            THE PCR PRIMERS DATABASE SUBMISSION FORM.


This is the data submission form for the PCR primers database.
It is basically intended for users who don't have access to a
WWW service and only have email.

If you can use a WWW browser, you are kindly requested to submit
your data through the WWW based submission system which can be 
found in:

http://www.ebi.ac.uk/primers_home.html



DISCLAIMER
This is the data submission form for the PCR primers database. By
filling the fields of this form and submitting it, you agree to the
following terms:

1.	The data hereby submitted is for public usage. There are no
	means of handeling confidential entries. Neither EBI or Benny
	Shomer or anyone else involved in maintaining the database
	may be assumed responsible for any consequences of releasing
	this data to the public.
	
2. 	The PCR primers database is provided on a non-commercial
	basis. No person is allowed to charge any price for the data,
	excluding the costs of the medium which holds the data (may
	it be charges for networking, disks or disk-space).

3.	The submitting author hereby declares that all the data
	submitted is correct and that the primers submitted were
	tested in the laboratory and were found to be functioning
	properly. It is also declared that the data is derived from
	an original work done by the author and / or colleagues who
	authorized the submission and that the data does not include
	any patented or commercial information without granted
	permission.
	

HOW TO FILL THE FORM?
When you submit information to our database, please bear in mind that
the whole purpose is establishing a PRACTICAL database which enables
researchers to synthesize primers based on the information you
provide and to be able to reconstitute your working environment. Be
precise, be complete, be honest.

Through the form, there are lines which contain remarks. These lines
are preceded with a hash mark (#). Please do not remove it, to enable
automatization of the data processing.

Please make an effort to adhere to the definitions. I currently
process the entries alone and time is unfortunately, not my best
friend :-(  Especially take care with measurments. Use the time,
volume, concentration measurments as requested and don't leave me to
do the translations for you. If people will fail to do so, I will lag
behind.

IMPORTANT NOTICE:  Allways start typing the information separated by a
space following the appropriate field name. In cases where your data is
longer than the remaining line, type it on the next consecutive lines.
Anything typed in between a field name and the one following it (excluding
the #hash marked lines) will be taken in.  If you want to provide
free-style comments which don't refer directly to the submission, type them
either before the $$$BEGIN DATA$$$  line, or after the terminator mark
(//).  If a requested data item is non-available, leave it empty. Don't
type anything like 'N/A' or 'non available' etc.  Some of the fields are
preceded by the remark  'Mandatory'.  The data for these fields must be
provided.


$$$BEGIN DATA$$$


# The amplification target. This may be a specification of a known gene 
# name, a chromosome and possibly the location on it etc. Specifying the
# organism here is optional. It may be multi line up to 250 characters.
#
# Mandatory

TARGET

# Specification of what do the sequence numbering and positions refer to.
# e.g. it could refer to position 1 on a cDNA, position 1 in a specific
# EMBL/Genbank/DDBJ entry etc.

NUMREF

# Organism Species. Defined according to the EMBL/Genbank/DDBJ  
# definitions.  Use the scientific name and put the common name
# in brackets.
#
# Mandatory

OSPECS

# Special applications. e.g. Cloning, Mutation etc.

SPAPLL

# At least one of the following two is mandatory
#
# Product length in base pairs when a cDNA is amplified.

LNCDNA

# Product length in base pairs when a Genomic DNA is amplified.

LNGDNA

# Name of the forward (5' --> 3') primer, assigned by the submitting 
# author.
#
# Mandatory

FPNAME

# Forward primer sequence, provided in 5' --> 3' direction (i.e. ready 
# for synthesis). Sequence therefore will be given only with 
# non-ambiguous bases. It will be displayed in triades, uppper case. 
#
# Mandatory

FPSEQN

# Flanking base on the target sequence. i.e. Which base on the target 
# sequence matches the first 5' base of the primer. This position will 
# be given with reference to the NUMREF field given earlier.

FFLANK

# Restriction site added to the primer sequence.

FRESTR

# Mutation introduced into the primer sequence. Will be expressed as
# base1 (or bases1) --> base2 (or bases2) in position, whereas base1
# is the  base(s) in the original sequence, base2 is the base(s) that
# were  introduced as a mutation and position is the position on the
# primer.

FMUTAT

# Unless this is a uni-directional reaction, the same fields are 
# mandatory here.

# Name of the reverse (3' --> 5') primer, assigned by the submitting 
# author.

RPNAME

# Reverse primer sequence, provided in 5' --> 3' direction (i.e. ready for
# synthesis). Sequence therefore will be given only with non-ambiguous 
# bases. It will be displayed in triades. 

RPSEQN

# See definition for FFLANK.

RFLANK

# See definition for FRESTR.

RRESTR

# See definition for FMUTAT.

RMUTAT

# Thermal Cycler make and model. Two fields separated by semicolon make;model
# if used more than one machine, you may provide the fields more than once.
#
# Mandatory

TCYCLE

# Temperature Sampling By Probe In-tube. A Boolean field accepting either 
# "YES" or "NO". 
#
# Mandatory

PROBIN

# Was the Hot-start protocol applied? A Boolean field accepting either "YES" 
# or "NO" (or leave empty = "NO")

HOTSTR


# Initial denaturation. Expressed as two fields separated by semicolon.
# Temperature in degrees centigrade ; duration in seconds.

IDENAT

# Denaturation. Expressed as two fields separated by semicolon.
# Temperature in degrees centigrade ; duration in seconds.
#
# Mandatory

DENATR

# Annealing.  Expressed as two fields separated by semicolon.
# Temperature in degrees centigrade ; duration in seconds.
#
# Mandatory

ANNEAL

# Touchdown protocol. Has two fields, separated by semicolon: Temperature 
# decrease in degrees centigrade; Number of cycles in which touchdown was
# applied.
	
TCHDWN

# Extension.  Expressed as two fields separated by semicolon.
# Temperature in degrees centigrade ; duration in seconds.

EXTEND

# Progressive extension. Has two fields, separated by semicolon: The time 
# added in seconds per cycle; The cycle number in which addition has started

PRGRSS

# Final extension step. Expressed as two fields separated by semicolon.
# Temperature in degrees centigrade ; duration in seconds.

FINEXT

# Total number of cycles per amplification reaction.
#
# Mandatory

CYCLES

# Total reaction volume expressed in microlitres.
#
# Mandatory

RXNVOL

# Polymerase used. Expressed as three fields separated by a semicolons: 
# Polymerase type; Polymerase make; Polymerase concentration in Units per
# reaction.
#
# Mandatory

POLYMR

# The type of buffer used. Can be either a commercially standard provided, in
# which case, the name of the provider is stated, or it can be one of a few 
# standard buffers of the database, or provided in full details.
#
# Mandatory
	
BUFFER

# Concentration of dNTP's in uM (micro molar). If all are the same, only one
# figure will be provided. Every dNTP with a different concentration follows
# separated by a semicolon.
#
# Mandatory

DNTPCN
	
# Concentration of primers in uM (micro molar). If both are the same, only one
# figure will be provided. Else, the concentration of each is provided followed 
# by the primer's name as appeared in FPNAME and RPNAME separated by a 
# semicolon.	
#
# Mandatory

PRIMCN	

# Concentration of MgCl2 in the buffer provided in mM (milimolar). Field will  
# be included only if the  MgCl2 concentration varied from a standard buffer 
# as defined in the BUFFER field. The figure provided will allways refer to 
# the final total concentration of Magnesium in the buffer.

MGCONC

# Various additives added to the reaction (e.g. DMSO, Formamide, Gelatin ). The
# units will be provided accordind to the submitters specifications. In the field
# the order will allways be additive name, concentration, units and be separated
# by a semicolon;

ADITIV	

# DNA Source, Method of Preparation and Amount added.		
#
# Mandatory

SOURCE

# Cross references for other databases. Expressed as: Database name followed by
# the acession numbers seperated by comma. Various databases separated with 
# semicolons. Database names according to pre-defined nomenclature.

DBXREF

# Names of contact author in the following format: Firstname
# Surname, separated by a comma.
#
# Mandatory

CNTNAM

# Institute of contact author
#
# Mandatory

CNTINS

# Regular mail address of contact author
#
# Mandatory

CNTADR

# Email address of contact author
#
# Mandatory

CNTEML

# Telephone number of contact author, including international dial code

CNTTEL

# Fax number of contact author, including international dial code

CNTFAX

# Reference author in the following format: Surname, Initials., 

REFAUT

# Reference title

REFTTL

# Reference publication line in the following format: Journal name
# according to the nomenclature defined for EMBL database folowed by
# Volume: frompage - topage, (Year)

REFSRC
	
# The name says it all... :-)  Anything that doesn't go into any of the 
# above fields, bu needs to go in.	

REMARK	

# The good old faithful record terminator. Please leave it untouched.	
	
//	
	
	
	
	



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