WormBase release WS87 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 WS87, Wormpep87 and Wormrna87 Wed Sep 25 13:31:54 BST 2002

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

This directory includes:

i)	database.WS87.*.tar.gz     -   compressed data for new release

ii)	models.wrm.WS87           -   the latest database schema (also in above database files)

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

iv)	WS87-WS86.dbcomp    -   log file reporting difference from last release

v)	wormpep87.tar.gz           -   full Wormpep distribution corresponding to WS87

vi)	wormrna87.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome

vii)	confirmed_genes.WS87.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 WS87
------------------------------------
brigdb : 2002-09-13 - updated
camace : 2002-09-16 - updated
citace : 2002-09-13 - updated
cshace : 2002-08-28
genace : 2002-09-16 - updated
stlace : 2002-09-13 - updated



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

       	WS87       	WS86      	change
----------------------------------------------
a    	32352971	32352971	  +0
c    	17772485	17772485	  +0
g    	17750022	17750022	  +0
t    	32354695	32354695	  +0
n    	95      	95      	  +0
-    	2000    	2000    	  +0

Total	100232268	100232268	  +0





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

There are 19483 CDS in autoace, 20881 when counting 1398 alternate splice forms.

The 20881 sequences contain 9,238,759 base pairs in total.

Modified entries               8
Deleted entries                7
New entries                   10
Reappeared entries             0

Net change  +3


GeneModel correction progress WS86 -> WS87
-----------------------------------------

Confirmed introns not is a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|   1545  |   -21  |
St Louis 	|    411  |    -1  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     26  |     0  |
St Louis 	|    181  |     0  |
		+---------+--------+


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

CHROMOSOME_III	sequence AF040644
----------------------------------------------------------------


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

# Gap on Chromosome III is covered by a 950Kb SseI fragment 

III     1005794 1028769 37      F       AC087078.1      1       22976   +
III     1028770 1029769 38      N       1000
III     1029770 1055632 39      F       AC092690.1      1       25863   +

# Gap on Chromosome X is 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       AC087735.3      1       11211   +


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

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


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


Other Changes:
--------------
As mentioned in the release notes for WS87, this build was the first to follow the rearranged protocol.
This means that all new proteins have been included in the WUBLAST analysis.


Proposed Changes / Forthcoming Data:
------------------------------------
We are planning to remove the EMBLace data (all EMBL: objects ) from the database.  They will be replaced by accession ID objects that contain the same ino and  the EMBL record as LongText.
Eg EMBL:AA545854 will be replaced by AA545854 .

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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