dbEST - database for "expressed sequence tags"

Francis Ouellette francis at borduas.nlm.nih.gov
Thu Jan 27 17:42:55 EST 1994


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	  dbEST - database for "expressed sequence tags"

		     Summary - January 21, 1994

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This is a regular announcement to indicate the status of dbEST at 
GenBank, National Center for Biotechnology Information (NCBI), 
National Library of Medicine, National Institutes of Health. 
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dbEST is a new resource (Nature Genetics 4:332-333; 1993) that contains 
data from labortories generating incomplete "single-pass" cDNA sequences 
(ESTs or "Expressed Sequence Tags," also known as "Transcribed Sequence 
Fragments" and "Putatively Transcribed Partial Sequences").

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:

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Date:                           1994-JAN-21

Database:                       dbEST
Database version number:        1.46
Number of Entries:              31,818


       	      Summary by Organism
	      ===================
	      Homo sapiens (human):                16933
	      Caenorhabditis elegans (nematode):    4699
	      Arabidopsis thaliana (thale-cress):   4512*
	      Oryza sativa (rice):                  4231*
	      Plasmodium falciparum (malaria):       831
	      Zea mays (maize):                      267*
	      Mus musculus+domesticus (mouse):       150
	      Capra hircus (goat):                   108
	      Pyrococcus furiosus:                    50
	      Macropus eugenii (marsupial):           36
	      Gallus gallus (chicken):                 1


* Note that we recently have received a large number of ESTs from
  several plant species.

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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)


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GenBank
National Center for Biotechnology Information 
Building 38A
National Library of Medicine, 
National Institutes of Health
Bethesda, MD, 20894, USA

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

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