Please, is it possible to download AtDB?

Mike Cherry cherry at genome.stanford.edu
Fri Apr 16 12:16:26 EST 1999


> > Federico,
> >
> > It depends on what you want.  Can you be more specific?  Much of AtDB
> > is within an object relational database.  We do not have method of
> > providing that information.
>
> I want to find transcription factors using tools as PSI-BLAST, BLAST, etc. I
> want to do felonies,
> so if I could have all the sequences of genes and ESTs and their identifiers,
> and maybe some description of them if available, it will be very good.

Federico,

You can download all the Arabidopsis sequences and other information
from our FTP site:

    ftp://genome-ftp.stanford.edu/arabidopsis/

This includes the full sequence set in the At_Genbank directory.  The
non-redundant protein set is in At_Protein directory.  Information
about the EST available from ABRC can be found in the ABRC directory.
Also check the AGI directory.  For all these directories please read
the README file.

> > However, much of AtDB is outside Illustra
> > managed by several other software packages.
>
> Which packages? Do you have an interface as SRS or similar to retrieve
> information?
>
> Federico

We use GCG and other tools for sequences, a variety of local tools to
create the Web graphics, a couple HTML indexing tools, the new map
displays are generated from data contained within an Oracle database.
We do not provide access via SRS.

However, in the near future we will be making more information
available via our ftp site.

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

> > > Hello everybody,
> > > I want to do some deep searches in the AtDB that are not possible trough
> > > the net, so I would like to have AtDB locally, is it possible?
> > > Please, send your answeres to email-address, if possible
> > > Thanks in advance,
> > > Federico




More information about the Arab-gen mailing list