WormBase release WS85 now online

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

New Release of acedb WS85, Wormpep85 and Wormrna85 020823
=========================================================

This directory includes:

i)	database.WS85.*.tar.gz     -   compressed data for new release

ii)	models.wrm.WS85            -   the latest database schema (also in above database files)

iii)	CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)

iv)	WS85-WS84.dbcomp           -   log file reporting difference from last release

v)	wormpep85.tar.gz           -   full Wormpep distribution corresponding to WS85

vi)	wormrna85.tar.gz           -   latest WormRNA release containing non-coding RNA's in the genome

vii)	confirmed_genes.WS85.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 WS85
------------------------------------
brigdb : 2002-08-16 - updated
camace : 2002-08-19 - updated
citace : 2002-08-16 - updated
cshace : 2002-08-14 - updated
genace : 2002-08-19 - updated
stlace : 2002-08-16 - updated


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

       	WS85       	WS84      	change
----------------------------------------------
a    	32344742	32344742	  +0
c    	17767680	17767680	  +0
g    	17745321	17745321	  +0
t    	32346297	32346297	  +0
n    	95      	95      	  +0
-    	62800   	62800   	  +0

Total	100266935	100266935	  +0

No net change to sequence.


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

There are 19479 CDS in autoace, 20844 when counting 1365 alternate splice forms.

The 20844 sequences contain 9,217,597 base pairs in total.

Modified entries              33
Deleted entries               32
New entries                   71
Reappeared entries             5

Net change  +44


GeneModel correction progress WS84 -> WS85
-----------------------------------------

Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|   1616  |   -28  |
St Louis 	|    463  |   -76  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     29  |     0  |
St Louis 	|    181  |     0  |
		+---------+--------+


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

CHROMOSOME_II	AF016683
CHROMOSOME_II	AL845469
CHROMOSOME_IV	AC006701
CHROMOSOME_IV	AC025724
CHROMOSOME_IV	AF125445
CHROMOSOME_IV	AF038618

----------------------------------------------------------------

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

Added features to the EST/mRNA sequences to indicate the oligo cap 
sequence and TSL sequences.
	 
	 No. of ESTs with Oligo_cap	     8567
	 No. of ESTs with SL1               14212
	 No. of ESTs with SL2 (& variants)   3195
	 
Added C.briggsae gene predictions to the ultracontigs. Predictions
using the following prediction algorithms have been added: genefinder,
fgenesh, twinscan and ensembl. 

New strains from the CGC.

New alleles from the knockout consortium.

New loci and gene classes.

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


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


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


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

New sequence data from St Louis to fill two of the remaining gaps.


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.

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