WormBase release WS90 now online

This is an automatic announcement that WormBase
(http://www.wormbase.org) has just been updated.  New releases occur
roughly every 2 weeks.

The text of the AceDB release notes, which contains highlights of the
new data is attached.  You can download the full AceDB files from:

   ftp://ftp.sanger.ac.uk/pub/wormbase/current_release/

New Release of acedb WS90, Wormpep90 and Wormrna90 Sun Nov 10 10:19:36 GMT 2002

>>> NOTE <<<
C. elegans Genome Sequence is Complete!

The WS90 release of WormBase made available today has a complete C. 
elegans genome sequence. The 100,258,171 base pairs are present in six 
contiguous segments corresponding to the six C. elegans nuclear 
chromosomes. On behalf of the C. elegans community we thank the C. 
elegans Genome Sequencing Consortium at the Wellcome Trust Sanger 
Institute and Washington University's Genome Sequencing Center for this 
impressive accomplishment.  In spite of the high quality of the 
sequence, there are undoubtedly remaining errors in the genome sequence, 
and thus the Sequencing Consortium will remain active in responding to 
and resolving any potential errors that arise. Please inform WormBase of 
any errors.

--Lincoln Stein and Paul Sternberg (for WormBase)

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

This directory includes:
i)	database.WS90.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS90           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir        -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS90-WS89.dbcomp          -   log file reporting difference from last release
v)	wormpep90.tar.gz          -   full Wormpep distribution corresponding to WS90
vi)	wormrna90.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS90.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA


Release notes on the web:
-------------------------
http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE



Primary databases used in build WS90
------------------------------------
brigdb : 2002-10-27 - updated
camace : 2002-11-06 - updated
citace : 2002-10-26 - updated
cshace : 2002-10-10
genace : 2002-10-30 - updated
stlace : 2002-10-28 - updated


Genome sequence composition:
----------------------------

       	WS90       	WS89      	change
----------------------------------------------
a    	32362216	32353009	+9207
c    	17777361	17772424	+4937
g    	17754941	17749963	+4978
t    	32363558	32354518	+9040
n    	95      	95      	  +0
-    	0       	2259    	-2259

Total	100258171	100232268	+25903




Wormpep data set:
----------------------------

There are 19488 CDS in autoace, 20970 when counting 1478 alternate splice forms.

The 20970 sequences contain 9,271,352 base pairs in total.

Modified entries             153
Deleted entries               56
New entries                   72
Reappeared entries             3

Net change  +19

Status of entries: Confidence level of prediction
-------------------------------------------------
Confirmed              3492 (16.7%)
Partially_confirmed    8661 (41.3%)
Predicted              8817 (42.0%)

Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2130 (10.2%)
TrEMBL accessions     18211 (86.8%)
TrEMBLnew accessions    478 (2.3%)

Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            20790 (99.1%)

Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection   3367


GeneModel correction progress WS89 -> WS90
-----------------------------------------
Confirmed introns not is a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|   1150  |  -103  |
St Louis 	|    324  |    18  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     27  |     0  |
St Louis 	|    103  |   -76  |
		+---------+--------+


Synchronisation with GenBank / EMBL:
------------------------------------

No synchronisation issues


Remaining gaps:
---------------
None!  The remaining St. Louis gaps have been finished and therefore this release of WormBase
contains the complete genome sequence, six contiguous chromosome sequences.


New Data:
---------


New Fixes:
----------


Known Problems:
--------------


Other Changes:
--------------


Proposed Changes / Forthcoming Data:
------------------------------------

Changes to Allele data to better integrate with Knockout Consortium strain and allele
information.


-===================================================================================-


Quick installation guide for UNIX/Linux systems
-----------------------------------------------

1. Create a new directory to contain your copy of WormBase,
	e.g. /users/yourname/wormbase

2. Unpack and untar all of the database.*.tar.gz files into
	this directory. You will need approximately 2-3 Gb of disk space.

3. Obtain and install a suitable acedb binary for your system
	(available from www.acedb.org).

4. Use the acedb 'xace' program to open your database, e.g.
	type 'xace /users/yourname/wormbase' at the command prompt.

5. See the acedb website for more information about acedb and
	using xace.

____________  END _____________