WormBase release WS114 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 WS114, Wormpep114 and Wormrna114 Fri Nov 14 10:30:51 GMT 2003


WS114 was built by Anthony
======================================================================

This directory includes:
i)	database.WS114.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS114           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir        -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS114-WS113.dbcomp          -   log file reporting difference from last release
v)	wormpep114.tar.gz          -   full Wormpep distribution corresponding to WS114
vi)	wormrna114.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS114.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii)	yk2orf.WS114.gz            -    Latest set of ORF connections to each Yuji Kohara EST clone
ix)	gene_interpolated_map_positions.WS114.gz    - Interpolated map positions for each coding/RNA gene
x)	clone_interpolated_map_positions.WS114.gz    - Interpolated map positions for each clone
xi)	best_blastp_hits.WS114.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.WS114.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 WS114
------------------------------------
brigdb : 2003-11-03 - updated
camace : 2003-11-04 - updated
citace : 2003-11-02 - updated
cshace : 2003-10-21 - updated
genace : 2003-11-07 - updated
stlace : 2003-11-03 - updated


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

       	WS114       	WS113      	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 19931 CDS in autoace, 22221 when counting 2290 alternate splice forms.

The 22221 sequences contain 9,696,145 base pairs in total.

Modified entries             109
Deleted entries               35
New entries                   31
Reappeared entries             5

Net change  +1



Status of entries: Confidence level of prediction (based solely on coverage by transcriptional data)
----------------------------------------------------------------------------------------------------
Confirmed              4644 (20.9%)     Every base has transcription evidence (mRNA, EST etc ).
Partially_confirmed   12121 (54.5%)	Some but not all bases are covered by transcript evidence.
Predicted              5456 (24.6%)	No transcriptional evidence at.


Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2455 (11.0%)
TrEMBL accessions     18798 (84.6%)
TrEMBLnew accessions    926 (4.2%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22177 (99.8%)



Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection   4507


GeneModel correction progress WS113 -> WS114
-----------------------------------------
Confirmed introns not is a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    652  |   -36  |
St Louis 	|    300  |  -115  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		|   Exons | Change |
		+---------+--------+
Cambridge	|      0  |     0  |
St Louis 	|     34  |     1  |
		+---------+--------+



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

No synchronisation issues


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



New Data:
---------
TrEMBL database updated to version 25 for blast analyses


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


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


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

Proposed Changes / Forthcoming Data:
------------------------------------
C. elegans PolyA sites and signals described in EMBL / Genbank / DBJJ mRNA entries will be incorporated in to WormBase from WS115

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


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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