WormBase release WS91 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 WS91, Wormpep91 and Wormrna91 Fri Nov 22 12:16:29 GMT 2002

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

This directory includes:
i)	database.WS91.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS91           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir        -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS91-WS90.dbcomp          -   log file reporting difference from last release
v)	wormpep91.tar.gz          -   full Wormpep distribution corresponding to WS91
vi)	wormrna91.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS91.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 WS91
------------------------------------
brigdb : 2002-11-08 - updated
camace : 2002-11-12 - updated
citace : 2002-10-26
cshace : 2002-11-05 - updated
genace : 2002-11-11 - updated
stlace : 2002-11-08 - updated


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

       	WS91       	WS90      	change
----------------------------------------------
a    	32362216	32362216	  +0
c    	17777360	17777361	  -1
g    	17754942	17754941	  +1
t    	32363558	32363558	  +0
n    	95      	95      	  +0
-    	0       	0       	  +0

Total	100258171	100258171	  +0




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

There are 19503 CDS in autoace, 21052 when counting 1545 alternate splice forms.

The 21052 sequences contain 9,305,386 base pairs in total.

Modified entries             155
Deleted entries               56
New entries                  134
Reappeared entries             4

Net change  +82

Status of entries: Confidence level of prediction
-------------------------------------------------
Confirmed              3540 (16.8%)
Partially_confirmed    8679 (41.2%)
Predicted              8833 (42.0%)

Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2009 (9.5%)
TrEMBL accessions     17825 (84.7%)
TrEMBLnew accessions    472 (2.2%)

Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            20900 (99.3%)

Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection   3377


GeneModel correction progress WS90 -> WS91
-----------------------------------------
Confirmed introns not is a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    939  |  -211  |
St Louis 	|    327  |     3  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     26  |    -1  |
St Louis 	|     65  |   -38  |
		+---------+--------+


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

No synchronisation issues
Following clones not in EMBL / GenBank as of release date

VY35H6BL   AL954367
CEXL	   AL954365
cTel7X	   AL031272
K04H4	   Z27078


Remaining gaps:
---------------
There are no gaps remaining in the genome sequence.
-===================================================================================-



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


New Fixes:
----------
The Drosophila proteins that were using old style names (pp-CTXXXX) have been updated and should now link correctly.


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


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

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


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


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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