WormBase release WS84 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 WS84, Wormpep84 and Wormrna84 Mon Aug 12 18:05:39 BST 2002

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

This directory includes:

i)	database.WS84.*.tar.gz     -   compressed data for new release

ii)	models.wrm.WS84           -   the latest database schema (also in above database files)

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

iv)	WS84-WS83.dbcomp    -   log file reporting difference from last release

v)	wormpep84.tar.gz           -   full Wormpep distribution corresponding to WS84

vi)	wormrna84.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome

vii)	confirmed_genes.WS84.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 WS84
------------------------------------
brigdb : 2002-08-05 - updated
camace : 2002-08-06 - updated
citace : 2002-08-06 - updated
cshace : 2002-06-30
genace : 2002-08-06 - updated
stlace : 2002-08-05 - updated



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

       	WS84       	WS83      	change
----------------------------------------------
a    	32344742	32344796	 -54
c    	17767680	17767733	 -53
g    	17745321	17745345	 -24
t    	32346297	32346366	 -69
n    	95      	95      	  +0
-    	62800   	62800   	  +0

Total	100266935	100267135	-200

Removal of 200bp due to correction of error where overlapping sequence
was duplicated.



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

There are 19476 CDS in autoace, 20800 when counting 1324 alternate splice forms.

The 20800 sequences contain 9,194,857 base pairs in total.

Modified entries             188
Deleted entries               51
New entries                  116
Reappeared entries             3

Net change  +68


GeneModel correction progress WS83 -> WS84
-----------------------------------------

Confirmed introns not is a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|   1644  |  -329  |
St Louis 	|    539  |  -144  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     29  |     0  |
St Louis 	|    181  |    -3  |
		+---------+--------+


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

CHROMOSOME_II	sequence AF016683
CHROMOSOME_II	sequence AF016683
CHROMOSOME_IV	sequence AC006701
CHROMOSOME_IV	sequence AC025724
CHROMOSOME_IV	sequence AC025724
CHROMOSOME_IV	sequence AF125445
CHROMOSOME_IV	sequence AF125445
----------------------------------------------------------------


Remaining gaps: 
---------------
For more info mail [email protected] 

# Gaps are covered by a 950Kb SseI fragment 

III      1005794   1028769   37  F    AC087078.1      1       22976  +
III      1028770   1029769   38  N                             1000
III      1029770   1075569   39  F    AC084156.1      1       45800  +

# Gaps are covered by YAC clones in production at St Louis

X              1      2649    1  F    AL031272.2      1       2649   +
X           2650      3649    2  N                            1000
X           3650     14860    3  F    AC087735.2      1       11211  +

X         177585    194657    6  F    AC084160.2      1       17073  +
X         194658    225057    7  N                            30400
X         225058    254821    8  F    Z83097.1        1       29764  +

X         225058    254821    8  F    Z83097.1        1       29764  +
X         254822    285221    9  N                            30400
X         285222    299761   10  F    AC024789.1      1       14540  +



New Data:
---------
updated Interpro and Pfam motifs

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


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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