WormBase release WS102 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 WormBase WS102, Wormpep102 and Wormrna102 Fri May 30 11:04:12 BST 2003


WS102 was built by Keith Bradnam who tackled 13 separate build-related problems

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

This directory includes:
i)	database.WS102.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS102           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir        -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS102-WS101.dbcomp          -   log file reporting difference from last release
v)	wormpep102.tar.gz          -   full Wormpep distribution corresponding to WS102
vi)	wormrna102.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS102.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 WS102
------------------------------------
brigdb : 2003-05-15 - updated
camace : 2003-05-20 - updated
citace : 2003-05-18 - updated
cshace : 2003-05-15 - updated
genace : 2003-05-23 - updated
stlace : 2003-05-15 - updated


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

       	WS102       	WS101      	change
----------------------------------------------
a    	32367166	32364258	+2908
c    	17780237	17778488	+1749
g    	17757588	17755882	+1706
t    	32368415	32365362	+3053
n    	95      	95      	  +0
-    	0       	0       	  +0

Total	100273501	100264085	+9416




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

There are 19575 CDS in autoace, 21643 when counting 2065 alternate splice forms.

The 21643 sequences contain 9,540,476 base pairs in total.

Modified entries             124
Deleted entries               41
New entries                   93
Reappeared entries             3

Net change  +55



Status of entries: Confidence level of prediction
-------------------------------------------------
Confirmed              3927
Partially_confirmed    8924
Predicted              8780 



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2321 (10.7%)
TrEMBL accessions     18106 (83.7%)
TrEMBLnew accessions   1200 (5.5%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            21627 (100.0%)



Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection   4221


GeneModel correction progress WS101 -> WS102
-----------------------------------------
Confirmed introns not is a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    496  |  -1039  |
St Louis 	|    144  |  -1209  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     26  |     1  |
St Louis 	|     24  |     0  |
		+---------+--------+



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

CHROMOSOME_X	sequence Z83097


There are no gaps remaining in the genome sequence
---------------

For more info mail [email protected]
-===================================================================================-



New Data:
---------
Clone AC8 has had an inverted repeat sequence unfolded which has caused the
genome sequence to gain about 10,000 bp.


New Fixes:
----------
Interpolated map positions now added for RNA genes in ?Transcript class


Known Problems:
--------------
Interpolated map positions still missing for miRNA genes.  Will be fixed for next release.


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

Proposed Changes / Forthcoming Data:
------------------------------------
Slight reorganisation of ?Laboratory class to more usefully store information about people who
work in CGC registered worm laboratories


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


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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