From: CHERRY@FRODO.MGH.HARVARD.EDU (Mike Cherry 726-5955)
Newsgroups: bionet.genome.arabidopsis
Subject: Arabidopsis Physical and Genetic Map
Date: 7 Sep 92 20:11:43 GMT
Distribution: bionet

Enhancement of AAtDB Gopher and WAIS servers:

The AAtDB Gopher and WAIS servers have been updated to include the
physical and genetic map of Arabidopsis. The entire physical map has
been converted to a text display. The genetic map is also available
via the AAtDB WAIS server or as a menu item in the Arabidopsis
Companion Gopher server. Examples of using the physical map are
included below. All Arabidopsis DNA sequences, not just the references
as previously available, have also been included in the AAtDB WAIS
server.

A brief overview of Internet Gopher: Internet Gopher provides a method
by which many different types of information located at disperse locations
can be connected together into a simple hierarchy of menus. The items
in the Gopher menus can represent any number of services including
Anonymous FTP servers, WAIS servers, and text or binary files. All of
these services can either be provided by the same computer used for
the Gopher server or provided by some other computer anywhere in the
world on The Internet.

A brief overview of WAIS: WAIS is an indexing and retrieval system
that allows very fast searches of large collections of information. To
conduct a search the user simply types in one or more words describing
the information they wish to retrieve. One current limitation of a
WAIS server is that the search only matches the full word. Thus a
search for angust returns no matches while angustifolia returns seven.

The AAtDB WAIS server has indexed every word present in the AAtDB
database.  The result of the search will list the entries that contain
at least one of the query words. The first word in the name of the
matching entries tells you the class of the information in AAtDB. The
Arabidopsis Research Companion is a Gopher Server that provides access
to the two WAIS servers dealing with Arabidopsis, the AAtDB and
Arabidopsis BioSci servers.

Internet Gopher and WAIS clients are available for a wide range of
computer types and require that the computer is connected to the
Internet. The best Gopher client I have seen was written by Don
Gilbert at Indiana University for the Macintosh and is called
GopherApp, (available via anonymous ftp from ftp.bio.indiana.edu in
the /util/gopher/gopherapp directory as a BinHex'd file
gopherapp.hqx).  A public access account is provided by the Department
of Molecular Biology at Massachusetts General Hospital for those
without the appropriate client software. This account is only
available via the Internet using telnet. From most Internet connected
computers issue the command "telnet ochre.mgh.harvard.edu", the
username is "gopher" and the password is "thaliana". A VT100 terminal
or emulator is assumed.  Once connected use the arrow keys to move up
or down in the menu. To select a menu item press return or the right
arrow key.

The AAtDB WAIS server is option number 2, the Arabidopsis BioSci list
is option number 3 and the Arabidopsis unified genetic map is
available under option number 4. Other Gopher servers at Indiana
University, EMBNet Switzerland, University of Houston and University
of Wisconsin follow next in the menu. Access to a few anonymous ftp
archives are next, then e-mail and weather forecast searches. The
final menu item is a document produced by the University of Minnesota,
the developers of Internet Gopher, that answers a lot of questions
about what gopher is and where to get the software.

Below are some examples of accessing the physical map information using the
AAtDB WAIS server.

Using the AAtDB WAIS server and searching for the RFLP g4111 will
produce a list of four matching entries:

	1. Chromosome : V.
	2. F2_data : "Goodman_5".
	3. Locus : "g4111".
	4. Strain : "CD2-31".

The first entry is the genetic map for chromosome V, which contains
g4111.  Then the entry for the primary F2 data for the Goodman lab
RFLPs on chromosome V. Next the Locus class entry for this RFLP.
Followed by the CD2-31 strain from the ABRC at Ohio State, which is
the cosmid clone 4111.

The genetic map listing includes the map distance and standard error
as produced by Dr. Piet Stam's JOINMAP program. The Unified Genetic
map is the result of a collaboration between Drs. Meyerowitz,
Koornneef and Goodman.

An example of the form of the genetic map:

Marker Name   Chrom       cM      Std Err
===========   =====     ======   ========
g2632           V        27.4      0.14
pGATC-11        V        27.5      0.08
g4560           V        27.9      0.05
g4111           V        28.0      0.08
pi              V        28.4      0.09
ms1             V        29.7      0.00
g4556           V        30.7      0.07


Here is the Locus : "g4111" entry which includes the genetic map
location, location of the F2 primary data and strain. Followed by the
physical map.  The EG* clones are YACs the others are cosmids.


Locus : "g4111"
Genetic Map	 V	cM: 28.0	Std Err: 0.08
F2_data	 "Goodman_5"
Strain	 "CD2-31"
Clone	 4111
Member of Contig: ctg689
Contig: ctg689 limits: -49 to 32

----------------------EG19E1----------------------
    --------------------------EG17E4--------------------------
                      ========4111========
                                ---------19793---------
                                   -----------17522-----------
                                      ----------10965----------
                                      ------------8330------------
                                            --------16187--------
                                               --------pOCA18Be--------
                                                  --------15121--------
                                                     ---------18816---------



Another example: Here EG13A2 was the word used to query WAIS.  Note in
this example the entire contig is not presented. The limits of the
view is indicated.


Clone : EG13A2
Member of Contig: ctg406
Contig: ctg406 limits: -134 to 191

Limits of this partial view are: -92 to 109

-------------------EG1C12-------------------
---6833---
 --11370--
    --19900--
     --------------------EG12f8--------------------
       --13655--
       ---------------EG10D9---------------
        --19439--
          ---8412---
           -----------------------EG18H3-----------------------
             =============EG13A2=============
                -----------------------------EG5C3---------------------------
                       -------7578-------
                              ---10414---
                                ---15274---
                                ----4941----
                                  ---13191---
                                     ---20023---
                                     ----12751----
                                      --chs--


The physical map view in the AAtDB WAIS is all text and thus limited
in the amount of information that can be displayed at once. The
physical map views only show ten clones on either side of the selected
cosmid or YAC. Thus if in the previous example of YAC EG13A2 you wish
to find the cosmids and YACs that overlap the left end of what is
displayed you could query WAIS for EG1C12 and view more of this contig
as shown here:


Clone : EG1C12
Member of Contig: ctg406
Contig: ctg406 limits: -134 to 191

Limits of this partial view are: -124 to 66

----4080----
  ---16327---
   ---19530---
    --17470--
    -----16847-----
     ----10827----
       ------16607%------
        ---16290---
           ---10825---
            -----6873-----
            =====================EG1C12=====================
             ---6833---
              --11370--
                  --19900--
                  ---------------------EG12f8---------------------
                    --13655--
                     ----------------EG10D9----------------
                     ---19439---
                        ---8412---
                         ------------------------EG18H3---------------------


You could also query for the contig name, ctg406 in the previous
example.  The result is a list of the members of the contig with their
positions, no picture is presented. You will also find "Clone" class
entries matching. These clones has not been associated with the
genetic map.

The workstation version of AAtDB, and the yet to be released Macintosh
version, provide much easier access to the physical map information.
You can get all the same information using the AAtDB WAIS its just
more work than using the ACeDB database software on a workstation.

If you have suggestions for how we can make these information servers
more useful or have problems connecting to or using the servers please
let me know.

The AAtDB project is funded by the U. S. Department of Agriculture
Plant Genome Research Program through the National Agricultural
Library. The Gopher and WAIS servers are provided by the Department of
Molecular Biology at Massachusetts General Hospital.

Mike Cherry
cherry@frodo.mgh.harvard.edu