update on dbEST

Francis Ouellette francis at BORDUAS.NLM.NIH.GOV
Thu Feb 24 14:19:10 EST 1994


Dear Arabidopsis-netters,

I just posted this message on a few of the relevant newsgroups, and I
noticed that the Arabidopsis community might be interested in knowing
that they now have the second largest number of ESTs in dbEST, after
having surpassed the nematodes in the last release of dbEST,

;-)

regards to all,

francis


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Bart Frank (frank at omrf.uokhsc.edu) writes on bionet.molbio.bio-matrix:

> Does someone know of an e-mail help service which could provide updated
> information on whether an est in genbank has been extended by the folks
> at the Institute for Genomic Research (TIGR)?

and on bionet.molbio.gdb:

> Is there an e-mail help service at The Center for Genomic Research?
> I'd like to know if additional sequence is available for one of the
> earlier relaeased versions of an est.

Bart,

Note that all publicly available EST sequences (Expressed Sequenced
Tags) are present in dbEST, the EST database maintained at NCBI
(GenBank).  This will include all publicly available EST sequences
from TIGR and other EST sequencing efforts.  The latest release for
dbEST is 1.52, and I append the latest stats on this release, as well
as some information on how to access this database.  If you have
further questions, do not hesitate to contact us.  For information on
TIGR's policy with respect to public release of their data, you might
try contacting mdadams at tigr.org.  Note that for many ESTs, the physical
DNA clones are available from the ATCC and other sources.  This information 
is contained in the dbEST records.

regards,

francis

--
| B.F. Francis Ouellette  
|
| francis at ncbi.nlm.nih.gov   




=========================================================================

	  dbEST - database for "expressed sequence tags"

		     Summary - February 15, 1994

=========================================================================

dbEST is a  resource (Nature Genetics 4:332-333; 1993) now in its second
year of operation that contains data from laboratories producing partial,
"single-pass" cDNA sequences (ESTs or "Expressed Sequence Tags").

Although dbEST sequences are incorporated into the new EST Division of
GenBank (Nucl. Acids Res. 21:2963-2965; 1993), annotation in dbEST is
more comprehensive and includes detailed contact information about the
contributors, genetic map locations (when available), and instructions
on obtaining physical DNA clones from the American Type Culture Collection
and other sources.  In addition, NCBI periodically updates putative
homology assignments using the BLAST family of programs after "filtering"
the ESTs to mask vector contamination, repetitive elements and low
complexity subsequences in the conceptual translations.

dbEST data is available in a variety of forms, described below.  

Information on the current release is as follows:

=====================================================================

Date:                           1994-FEB-15

Database:                       dbEST
Database version number:        1.52
Number of Entries:              32,276


       	      Summary by Organism
	      ===================


Homo sapiens (human):					16943
Arabidopsis thaliana (thale cress):			 4756
Caenorhabditis elegans (nematode):			 4699
Oryza sativa (rice):					 4342
Plasmodium falciparum (malaria parasite):		  831
Zea mays (maize):					  341
Mus musculus+domesticus (mouse):			  150
Capra hircus (goat):					  108
Pyrococcus furiosus (hyperthermophilic archaeon):	   50
Macropus eugenii (tammar wallaby):			   36
Gallus gallus+domesticus (chicken):			   20



======================================================================

ACCESS TO EST DATA


1) The nucleotide sequences may be searched using the BLAST electronic
   mail server.  For more information send an e-mail message with the
   word "help" in the body of the message to blast at ncbi.nlm.nih.gov.
   The TBLASTN program wich takes an amino acid query sequence and
   compares it with six-frame translations of dbEST DNA sequences is
   particularly useful.

2) Full reports on ESTs, including homology data, can be retrieved from 
   the dbEST electronic mail server.  For more information send an 
   e-mail message with the word "help" in the body of the message to 
   est_report at ncbi.nlm.nih.gov

3) EST sequences are included in the new EST division of GenBank (R) 
   available from NCBI on CD-ROMs and by anonymous ftp. Individual records
   may be retrieved using the RETRIEVE electronic mail server.  For more
   information send an e-mail message with the word "help" in the body of 
   the message to retrieve at ncbi.nlm.nih.gov

4) EST sequences are also available as a flat file in the FASTA format by
   anonymous FTP in the /repository/dbEST directory at ncbi.nlm.nih.gov

5) We are also planning for Gopher amd WWW access to EST information.  See 
   future postings of this announcement and "NCBI News."  (For a free
   subscription, send a request along with your name and postal mailing 
   address to: info at ncbi.nlm.nih.gov)


==========================================================================

GenBank
National Center for Biotechnology Information 
Building 38A, Rm 8N-803
National Library of Medicine, 
National Institutes of Health
Bethesda, MD, 20894, USA

telephone:	+1 (301) 496-2475
fax:		+1 (301) 480-9241
e-mail: info at ncbi.nlm.nih.gov
WWW URL: http://www.ncbi.nlm.nih.gov

==========================================================================



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