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Forest Tree RAPD Data Wanted

Bradley K. Sherman bks at s27w007.pswfs.gov
Thu Nov 18 14:17:46 EST 1993



Introduction

Dendrome is a forest tree genome informatics and database
project.  The Institute of Forest Genetics, USDA Forest
Service, Albany CA is overseeing the project in
collaboration with the National Agricultural Library.
TreeGenes is the central database and it is intended that
this database include genetic maps and associated
information for all forest trees.  At this time, we are
focusing our efforts on collecting RAPD map data.  This
announcement is a request to tree genome researchers to
submit RAPD map data for inclusion into the database.
These data will be made publically available through
distribution of the TreeGenes database. 

Contributors are encouraged to submit unpublished data but
have the option of completely selected fields of the input
file.  Please contact David Neale or Bradley Sherman
(contact information below) if you have any questions
regarding submission of your data to the TreeGenes
database.  We look forward to your submissions and the
development of a rich forest tree genome database for the
forest genetics research community.


Accepted Formats

We are prepared to accept your data in almost any format.
Below is a sample data file, but we would rather have your
submission sooner, in your own format, than later in ours.
If you do submit data in a local format please include
a description of the meaning of the data, computer platform
used and a contact person for clarification.  Data may be
submitted by FTP, email, or on diskette.


For More Information

David B. Neale (dbn at s27w007.pswfs.gov)
Bradley K. Sherman (bks at s27w007.pswfs.gov)
Institute of Forest Genetics
USDA Forest Service
P.O. Box 245, Berkeley, CA, 94701
Phone (510)559-6437  FAX (510)559-6440


Sample Submission

A Sample file showing preferred format follows.  Any line
beginning with a sharp '#' is a comment.  Please feel free
to include as many comments as you like in a submission.
We have indented all of the comments below, although this
is not required.  Each field is preceded by a comment
which shows some sample data.

Question marks '?' show where your data should go.
Data tags are separated from the data by colons ':'.
----------------------Begin Sample File----------------------------
       #
       #  A Sample file demonstrating how to
       #  submit data concerning a  RAPD map
       #  to the TreeGenes database.
       #
       #  This is an attempt at an inclusive file,
       #  you may wish to omit certain sections.
       #
       # The general rule is that a line  has a tag name and a
       # value separated by a colon ':'
       #
       #
       # Give Latin name. For Hybrid show both species.
       # Species : Pinus taeda
Species : ?

       # Tell us who you are and where you live
       # In the Laboratory Section. Use as many lines
       # As you like.
       # Laboratory : Institute of Forest Genetics
       # Laboratory : USDA Forest Service
       # Laboratory : P.O. Box 245, Berkeley, CA, 94701
       # Laboratory : Phone 510-559-6347
       # Laboratory : FAX 510-559-6440
Laboratory : ?
Laboratory : ?
Laboratory : ?

       # You may choose a Laboratory ID (3 letters) and an
       # Experiment ID (3 letters) or we will do it for you.
       # We use these do disambiguate data from different
       # laboratories and different experiments within
       # laboratories:
       # Laboratory ID : IFG
       # Experiment ID : QTL
Laboratory ID : ?
Experiment ID : ?

       # Name the investigators for the experiment
       # Use as many lines as you like:
       # Investigator : David B. Neale
       # Investigator : Andrew T. Groover
       # Investigator : Kathy D. Jermstad
Investigator : ?
Investigator : ?

       # Give the name of a contact for data clarification:
       # Contact : Bradley K. Sherman
       # Contact : (510) 559-6437
       # Contact : bks at s27w007.pswfs.gov
Contact : ? 
Contact : ?
Contact : ?

       # If the map is published please give a citation
       # Paper : Groover, A.T., Jermstad, K.D. and Neale, D.B. (1999),
       # Paper : Genetics 411, 441-449.
Paper : ?


       # Assign a descriptive name to the Genetic map:
       # Map : Loblolly Pine RAPD Base Map
Map : ?

       # Describe the mapping population used in the
       # experiment; if a single tree give name of tree.
       # Specify number of individuals used.
       #
       # Mapping population :  Single tree map from loblolly pine
       # Mapping population :  tree 7-56.  60 megagametophytes
       # Mapping population :  in segregating population.
Mapping population : ? 
Mapping population : ?

       # How many Linkage groups and loci are there in your map?
       # This serves to double check the data entry process:
       # Total linkage groups : 3
       # Total loci : 18
Total linkage groups : ?
Total loci : ?

       # Candidates for units of distance on the map are, e.g.
       # recombination, centimorgan/Kosambi, centimorgan/Haldane:
       # Units : recombination
Units : ?

       #  The Genetic Map itself.
       #  The Genetic Map is composed of Linkage groups
       #  In the file the Linkage groups are separated from
       #  one another by at least one blank line.
       #  Give the name of the group the number of loci, then
       #  List the Loci with primer name, molecular weight and position
       #    and an error estimate.  Please use a '-' for missing values.
       #    If you do not have an error estimate you may omit the fourth
       #    field.
       #
       #  If you are using a primer that is not from UBC or Operon
       #      please give its sequence as the locus name
       #
       #  Note that positions are cumulative, not pairwise, distances!
       #
       #
       # Linkage group : QTL-1
       # Number of loci : 10
       # Locus : OPA-1    800  0.0
       # Locus : OPD-3    750  15.1
       # Locus : OPX-3    1250 15.9
       # Locus : OPC-3    900  23.8
       # Locus : OPN-3    775  50.0
       # Locus : OPAA-3   625  55.2
       # Locus : OPAD-3   700  55.2
       # Locus : UBC-351  1180 70.1
       # Locus : OPB-4    1500 80.8
       # Locus : OPB-9    300  85.8
       # 
       # Leave a blank line between but not within linkage groups.
       # Linkage group : QTL-2
       # Number of loci : 3
       # Locus : OPA-1    550  0.0
       # Locus : OPA-5    375  20.3
       # Locus : OPAX-1   975  22.8
       # 
       #        # Here is the 3rd linkage group.
       # Linkage group : QTL-5
       # Number of loci : 5
       # Locus : UBC-325    550  0.0
       # Locus : UBC-550    375  20.3
       # Locus : UBC-220    975  22.8
       # Locus : UBC-340    850  22.8
       # Locus : OPA-1      700  30.8
Linkage group : ?
Number of loci : ?
Locus : ?
Locus : ?
Locus : ?
Locus : ?
Locus : ?

Linkage group : ?
Number of loci : ?
Locus : ?
Locus : ?
Locus : ?
Locus : ?
Locus : ?


       # Take as many or as few lines to describe your protocols
       # as you like.  Please bracket this section by the tags
       # "Begin protocol :" and "End protocol : "
       #  You may have multiple protocol sections if you like.:
       # Begin protocol:
       # 
       # RAPD Reaction and Cycling Conditions
       # 
       # This protocol was originally derived from the Perkin-Elmer
       # protocol for PCR amplification of DNA and then modified at
       # the Institute of Forest Genetics by various scientists.
       # 
       #  [...]
       # 
       # Perkin-Elmer reaction:
       # 100 ul reaction scaled down to 25 ul;
       # 
       # 10x PCR buffer                       25 ul          1x
       # dNTP mix (1.25 mM each dNTP)          4 ul          200 uM
       # primer [10 mM]                        1 ul          0.4 uM
       # Taq polymerase (reduced amt)        0.2 ul          1.0 units
       # Tween 20                           0.13 ul          0.5 %
       # 
       #  [...]
       # 
       # End protocol :
Begin protocol :
 ?
 ?
End protocol :


       # What software and hardware did you use?
       # Linkage analysis software : Mapmaker 2.0
       # Hardware platform : Sun Microsystems SPARCstation

Linkage analysis software : ?
Hardware platform : ?

       # Following this please provide input file for the
       # linkage analysis program.  It can be submitted in
       # a separate file if you like.  Please bracket the
       # beginning and end of the file with the labels
       # "Begin input file" and "End input file":
       #
       # Begin input file :
       # * FAMILY LIST
       # *884  abc def jek [...]
       # 
       #    [...]
       # 
       # *LOCUS NAME OP-A1-800
       # *ABBREVIATION OPA1_800
       # 
       #    [...]
       # 
       # *END
       # End input file :
Begin input file :
 ?
 ?
End input file :
----------------End of sample submission file------------------

-- 
Bradley K. Sherman               P.O. Box 245                    
Computer Scientist               Berkeley, CA, 94701
Dendrome Project                 510-559-6437 FAX: 510-559-6440  
Institute of Forest Genetics     Internet: bks at s27w007.pswfs.gov



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