gene or enzyme standard categories

Mike Cherry cherry at genome.Stanford.EDU
Thu Mar 9 11:59:40 EST 2000


Laura,

If what you seek is the identification on yeast genes you can use a
the Saccharomyces Genome Database (SGD) resource.  We provide several
downloadable tables that contain information on all standard yeast
genes.  If you are just interested in protein encoding genes the files
in the following directory might be of use to you.

  ftp://genome-ftp.stanford.edu/yeast/tables/ORF_Descriptions/

a text and TAB version is available.

The orf_descriptions.txt file contains the columns: 
        ORF  Gene  Process  Function
The Process and Function columns are now truncated to 30 characters.

The orf_descriptions.tab file contains the columns: 
        ORF  Gene  Length  Process  Function  SGDID
Length and SGDID are new columns.  No columns are truncated.

You can also browse the SGD database starting at:

  http://genome-www.stanford.edu/cgi-bin/SGD/search

the main home for SGD is at:

  http://genome-www.stanford.edu/Saccharomyces/

SGD also provides a BLAST resource.  The output provides links into
the database, and to others where appropriate.

  http://genome-www2.stanford.edu/cgi-bin/SGD/nph-blast2sgd

Mike

J. Michael Cherry, Ph.D.         Internet: cherry at genome.stanford.edu
Department of Genetics           Stanford University School of Medicine
Medical Center, Room M341        Stanford, California  94305-5120
Voice:    650-723-7541           FAX: 650-723-7016


> 
> I am trying to categorize BLAST results into gene/enzyme/metabolic
> categories.  Does anyone know of a reference that gives standards used in
> yeast and/or E. coli for such categories.  I have searched a number of the
> bionet archives to no avail after seeing mention of such a reference a few
> weeks ago.  Thanks for any information you might have.
> 
> Laura Fredrick Marek
> Iowa State University
> lmarek at iastate.edu
> 
---





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