WormBase release WS115 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 WS115, Wormpep115 and Wormrna115 Fri Nov 28 16:11:56 GMT 2003


WS115 was built by [email protected]
======================================================================

This directory includes:
i)	database.WS115.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS115           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir        -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS115-WS114.dbcomp          -   log file reporting difference from last release
v)	wormpep115.tar.gz          -   full Wormpep distribution corresponding to WS115
vi)	wormrna115.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS115.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii)	yk2orf.WS115.gz            -    Latest set of ORF connections to each Yuji Kohara EST clone
ix)	gene_interpolated_map_positions.WS115.gz    - Interpolated map positions for each coding/RNA gene
x)	clone_interpolated_map_positions.WS115.gz    - Interpolated map positions for each clone
xi)	best_blastp_hits.WS115.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.WS115.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 WS115
------------------------------------
brigdb : 2003-11-17 - updated
camace : 2003-11-17 - updated
citace : 2003-11-16 - updated
cshace : 2003-10-21
genace : 2003-11-18 - updated
stlace : 2003-11-17 - updated


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

       	WS115       	WS114      	change
----------------------------------------------
a    	32368607	32368607	  +0
c    	17780992	17780992	  +0
g    	17758424	17758424	  +0
t    	32369797	32369797	  +0
n    	95      	95      	  +0
-    	0       	0       	  +0

Total	100277915	100277915	  +0




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

There are 19892 CDS in autoace, 22227 when counting 2335 alternate splice forms.

The 22227 sequences contain 9,724,775 base pairs in total.

Modified entries             129
Deleted entries               87
New entries                   90
Reappeared entries             3

Net change  +6



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              4658 (21.0%)	Every base has transcription evidence (mRNA, EST etc )
Partially_confirmed   12164 (54.7%)	Some but not all bases are covered by transcript evidence
Predicted              5405 (24.3%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2443 (11.0%)
TrEMBL accessions     18591 (83.6%)
TrEMBLnew accessions   1158 (5.2%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22190 (99.8%)



Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection   4529


GeneModel correction progress WS114 -> WS115
-----------------------------------------
Confirmed introns not is a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    406  |  -246  |
St Louis 	|    221  |   -79  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|      0  |     0  |
St Louis 	|     36  |     2  |
		+---------+--------+



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

CHROMOSOME_III	sequence L10986
CHROMOSOME_III	sequence L10986

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



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

Sequence objects representing old and removed gene predictions (Method = history) are included.

Some polyA_site and poly_signal features from the nucleotide database (EMBL/GenBank/DDBJ) have been 
included in the Feature class.


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


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


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

Proposed Changes / Forthcoming Data:
------------------------------------
New CDS model paving the way to new gene model of Wormbase will be used in WS116.

WS116 may only be viewed on the live site (http://www.wormbase.org) at the beginning of 2004 due to 
model change which would need prolonged period of testing on the dev site (http://dev.wormbase.org).

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


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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