WormBase release WS120 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 WS120, Wormpep120 and Wormrna120 Mon Mar  1 15:53:31 GMT 2004


WS120 was built by [email protected]
======================================================================

This directory includes:
i)	database.WS120.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS120           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir        -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS120-WS119.dbcomp          -   log file reporting difference from last release
v)	wormpep120.tar.gz          -   full Wormpep distribution corresponding to WS120
vi)	wormrna120.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS120.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii)	yk2orf.WS120.gz            -    Latest set of ORF connections to each Yuji Kohara EST clone
ix)	gene_interpolated_map_positions.WS120.gz    - Interpolated map positions for each coding/RNA gene
x)	clone_interpolated_map_positions.WS120.gz    - Interpolated map positions for each clone
xi)	best_blastp_hits.WS120.gz    - for each C. elegans WormPep protein, lists Best blastp match to
 
                                        human, fly, yeast, C. briggsae, and SwissProt & Trembl proteins.
xii)	best_blastp_hits_brigprot.WS120.gz   - for each C. briggsae protein, lists Best blastp match to
 
                                        human, fly, yeast, C. elegans, and SwissProt & Trembl proteins.


Release notes on the web:
-------------------------
http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE



Primary databases used in build WS120
------------------------------------
brigdb : 2004-02-15 - updated
camace : 2004-02-17 - updated
citace : 2004-02-13 - updated
cshace : 2004-02-15 - updated
genace : 2004-02-20 - updated
stlace : 2004-02-15 - updated


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

       	WS120       	WS119      	change
----------------------------------------------
a    	32368547	32368630	 -83
c    	17781234	17781015	+219
g    	17758249	17758448	-199
t    	32369937	32369814	+123
n    	8       	8       	  +0
-    	0       	0       	  +0

Total	100277975	100277915	 +60




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

There are 19889 CDS in autoace, 22246 when counting 2357 alternate splice forms.

The 22246 sequences contain 9,745,258 base pairs in total.

Modified entries              32
Deleted entries               13
New entries                   18
Reappeared entries             2

Net change  +7



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              4855 (21.8%)	Every base has transcription evidence (mRNA, EST etc )
Partially_confirmed   12048 (54.2%)	Some but not all bases are covered by transcript evidence
Predicted              5343 (24.0%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2477 (11.1%)
TrEMBL accessions     18451 (82.9%)
TrEMBLnew accessions   1234 (5.5%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22161 (99.6%)



Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection   4935


GeneModel correction progress WS119 -> WS120
-----------------------------------------
Confirmed introns not is a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    438  |    29  |
St Louis 	|    264  |    27  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|      0  |     0  |
St Louis 	|     37  |     0  |
		+---------+--------+



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

CHROMOSOME_II	sequence Z46676

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



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

(1) CDS gi numbers linked to GeneBank
(2) Briggsae BACends data 
(3) Automatic assignment of GO terms based on RNAi phenotypes
(4) Operon data updated
(5) Large scale allele (tmxxx) info with sequence information from National Bioresource Project in Japan 
    See http://www.grs.nig.ac.jp/c.elegans/index.jsp?lang=english (under Mutant DB)



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.

____________  END _____________