WormBase release WS96 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 WS96, Wormpep96 and Wormrna96 Thu Feb 20 16:04:43 GMT 2003

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

This directory includes:
i)	database.WS96.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS96           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir        -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS96-WS95.dbcomp          -   log file reporting difference from last release
v)	wormpep96.tar.gz          -   full Wormpep distribution corresponding to WS96
vi)	wormrna96.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS96.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 WS96
------------------------------------
brigdb : 2003-02-10 - updated
camace : 2003-02-13 - updated
citace : 2003-02-09 - updated
cshace : 2003-01-26
genace : 2003-02-13 - updated
stlace : 2003-02-10 - updated


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

       	WS96       	WS95      	change
----------------------------------------------
a    	32364259	32364257	  +2
c    	17778485	17778485	  +0
g    	17755881	17755882	  -1
t    	32365361	32365361	  +0
n    	95      	95      	  +0
-    	0       	0       	  +0

Total	100264081	100264080	  +1




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

There are 19536 CDS in autoace, 21420 when counting 1880 alternate splice forms.

The 21420 sequences contain 9,452,721 base pairs in total.

Modified entries              65
Deleted entries               57
New entries                  134
Reappeared entries             2

Net change  +79



Status of entries: Confidence level of prediction
-------------------------------------------------
Confirmed              3728 (17.4%)
Partially_confirmed    8893 (41.5%)
Predicted              8799 (41.1%)



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2064 (9.6%)
TrEMBL accessions     18090 (84.5%)
TrEMBLnew accessions    925 (4.3%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            21079 (98.4%)



Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection   4174


GeneModel correction progress WS95 -> WS96
-----------------------------------------
Confirmed introns not is a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|   1666  |   995  |
St Louis 	|    158  |     6  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     24  |     0  |
St Louis 	|     24  |     0  |
		+---------+--------+



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

CHROMOSOME_X	sequence U49943
CHROMOSOME_X	sequence U49943
CHROMOSOME_X	sequence U49943

There are no gaps remaining in the genome sequence
---------------
For more info mail [email protected]
-===================================================================================-



New Data:
---------
Protein databases used for Blast analysis were:
  Gadfly 3.1
  Ensemble Human 10.30.1
  
New Fixes:
----------


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


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


Proposed Changes / Forthcoming Data:
------------------------------------
New feature class for Sequence 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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