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Mary Berlyn mary at FETALPIG.BIOLOGY.YALE.EDU
Fri Jul 8 10:51:46 EST 1994


Perhaps the following reply to Peta Bonham-Smith is of interest to
other 'rabids as well.

-------------------Posted Msg---------------------------------------
Date: 7 Jul 1994 09:07:06 -0700
From: "Bonham, Peta" <pbonham at pbi.nrc.ca>
To: arabidopsis at net.bio.net
Subject: To complement an auxotroph

Hello Arabnetters:
I would like to complement an Arabidopsis auxotroph with the bacterial 
equivalent gene.  How can I find out which bacterial genes have been cloned?
Is there a listing and depository for them?
Thanks
Peta Bonham-Smith
pbonham at pbi.nrc.ca
--------------------------------------------------------------------

The E.coli Genetic Stock Center database does not track all bacterial
genes that have been cloned, nor even all E.coli clones, but we do
keep records on and distribute the Clarke and Carbon clones. For
Kohara Lambda clones, contact Kenn Rudd at NCBI (rudd at ncbi.nlm.nih.gov).
There are other distributors of Kohara clones in US and elsewhere.
The information in the CGSC db can be accessed via a gopher server 
(e.g., UMn -> Connecticut), via a guest login to our sybase database
(read "About..." and "How to Access.." files in the gopher and write for
a p'wd.), or via WorldWideWeb/Mosaic, http://cgsc.biology.yale.edu/top.html.
-Mary Berlyn
--------------------------------------------------------------------
Examples of finding plasmid info, if you're interested:
On the gopher, if you wanted to see if we had a plasmid containing, e.g.,
nadC, you could select #3=Sites (Genes, Operons,...) on the menu and
enter nadC as the word to search for; it would return the gene, two
deletion fragments, and a plasmid, pLC37-40.  To get the plasmid, send me 
email or call or whatever. If you don't know the gene name, you can search for
gene product name or EC#, or you can go to the sybase interface or
the web and there use the form-based complex-query interfaces that would
allow you to enter your specifications in the appropriate, labelled fields.
For example, if you wanted the enolase encoding gene, a gopher search could
first retrieve the gene name if you search the Site files for "enolase" 
(where it appears as GeneProduct of the eno gene) and  then search on 
"eno" or "eno and plasmid" to retrieve 2 plasmids. As guest in the sybase 
database, aptforms interface, you could go to the SITE form, enter
Type: plasmid and find on the middle of the form the Subsites field,
actually labeled "Sites", place your cursor in that field and select
"Sub!" (for subquery) on the menu bar. This brings up another SITE form 
corresponding to that subsites field where you would describe the subsite
you want in the fields Type: Gene, and Product: enolase.   "Go!" on the 
menu bar then returns the proper gene, eno, to the (Sub-)Sites field on
the SITE form and a "Go!" command there brings up the names of the
two plasmids, and you can then examine their description. [Had you wanted
a more indirect query than that, say by EC# rather than name of the product, 
you could have done a further "Sub" on the Product field to enter EC#.] 
The web server is new and not all the sybase fields or special features 
have yet been incorporated, but it has the advantage of hypertext links 
within the db and to other db's (e.g. Product.EC# -> ENZYME DB).
If you try any of these modes of using the database and have difficulty,
please feel free to contact me with questions (or complaints).






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