From usenet.ucs.indiana.edu!sol.ctr.columbia.edu!spool.mu.edu!agate!ames!ig!bionet!FRODO.MGH.HARVARD.EDU!CHERRY Mon Sep 7 15:34:58 EST 1992 Article: 141 of bionet.genome.arabidopsis Path: usenet.ucs.indiana.edu!sol.ctr.columbia.edu!spool.mu.edu!agate!ames!ig!bionet!FRODO.MGH.HARVARD.EDU!CHERRY From: CHERRY@FRODO.MGH.HARVARD.EDU (Mike Cherry 726-5955) Newsgroups: bionet.genome.arabidopsis Subject: Arabidopsis Physical and Genetic Map Message-ID: <920907161143.2060621d@Frodo.MGH.Harvard.EDU> Date: 7 Sep 92 20:11:43 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 215 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