WormBase release WS89 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 WS89, Wormpep89 and Wormrna89 Fri Oct 25 10:12:02 BST 2002

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

This directory includes:
i)	database.WS89.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS89           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir        -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS89-WS88.dbcomp          -   log file reporting difference from last release
v)	wormpep89.tar.gz          -   full Wormpep distribution corresponding to WS89
vi)	wormrna89.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS89.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 WS89
------------------------------------
brigdb : 2002-10-11 - updated
camace : 2002-10-17 - updated
citace : 2002-10-13 - updated
cshace : 2002-10-10 - updated
genace : 2002-10-14 - updated
stlace : 2002-10-11 - updated


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

       	WS89       	WS88      	change
----------------------------------------------
a    	32353009	32352971	 +38
c    	17772424	17772485	 -61
g    	17749963	17750022	 -59
t    	32354518	32354695	-177
n    	95      	95      	  +0
-    	2259    	2000    	+259

Total	100232268	100232268	  +0

Telomeric clone cTel7X was reverse-complemented and clipped to remove chimeric
sequence and vector contamination.

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

There are 19508 CDS in autoace, 20951 when counting 1443 alternate splice forms.

The 20951 sequences contain 9,266,692 base pairs in total.

Modified entries              29
Deleted entries               15
New entries                   33
Reappeared entries             2

Net change  +20

Status of entries: Confidence level of prediction
-------------------------------------------------
Confirmed              3460 (16.5%)
Partially_confirmed    9126 (43.6%)
Predicted              8365 (39.9%)

Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2093 (10.0%)
TrEMBL accessions     17797 (84.9%)
TrEMBLnew accessions    845 (4.0%)

Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            20713 (98.9%)

Wormpep proteins linked to Locus
---------------------------------------------
Entries with locus connection   3358


GeneModel correction progress WS88 -> WS89
-----------------------------------------
Confirmed introns not is a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|   1253  |   -45  |
St Louis 	|    306  |   -52  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     27  |    -1  |
St Louis 	|    179  |    -1  |
		+---------+--------+


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

No synchronisation issues


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:
---------
- Updated Ensemble human protein dataset for blastP/X

New Fixes:
----------
- Fixed prefix of Gadfly protein entries
- Removed EMBL prefix of sequences crossed referenced from Caltech

Known Problems:
--------------
- some RNAi objects from csh (extra large coordinates, > 1 Mb)

Other Changes:
-------------
- Removed deprecated nematode ESTs consensus seqeunces.

Proposed Changes / Forthcoming Data:
------------------------------------
- Improve the quality of timestamps to display each object with its source database 
wherein timestamps made by cross-reference will maintain the source primary database
name (i.e. caltech/camace/stlace/csh).


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


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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