WormBase release WS118 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 WS118, Wormpep118 and Wormrna118  January 30th

WS118 was built by me
======================================================================

This directory includes:
i)	database.WS118.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS118           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS118-WS117.dbcomp         -   log file reporting difference from last release
v)	wormpep118.tar.gz          -   full Wormpep distribution corresponding to WS118
vi)	wormrna118.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS118.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii)	yk2orf.WS118.gz            -    Latest set of ORF connections to each Yuji Kohara EST clone
ix)	gene_interpolated_map_positions.WS118.gz    - Interpolated map positions for each coding/RNA gene
x)	clone_interpolated_map_positions.WS118.gz   - Interpolated map positions for each clone
xi)	best_blastp_hits.WS118.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.WS118.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 WS118
------------------------------------
brigdb : 2004-01-15 - updated
camace : 2004-01-21 - updated
citace : 2004-01-18 - updated
cshace : 2003-11-26
genace : 2004-01-22 - updated
stlace : 2004-01-16 - updated


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

       	WS118       	WS117      	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 19890 CDS in autoace, 22237 when counting 2347 alternate splice forms.

The 22237 sequences contain 9,731,099 base pairs in total.

Modified entries              69
Deleted entries               32
New entries                   33
Reappeared entries             9

Net change  +10



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              4848 (21.8%)	Every base has transcription evidence (mRNA, EST etc )
Partially_confirmed   12044 (54.2%)	Some but not all bases are covered by transcript evidence
Predicted              5345 (24.0%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2450 (11.0%)
TrEMBL accessions     18490 (83.1%)
TrEMBLnew accessions   1238 (5.6%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22177 (99.7%)



Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection   4895


GeneModel correction progress WS117 -> WS118
-----------------------------------------
Confirmed introns not is a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    436  |   -31  |
St Louis 	|    267  |   -90  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

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

15,900 new EST sequences. These are 5' single reads from the cDNA clones used in the 
interacteome project from the Vidal lab. Currently, we ahve dealt with these as EST
sequences in WormBase.

1330 TEC-RED trans-splice leader acceptor sites from Hwang, Muller and Sternberg. A
further 31 tags need clarification due to multiple matches in the genome preventing a
unique mapping of the tag sequence.


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

The C.briggsae gene predictions (all ab initio predictions and the hybrid set) have been
corrected for the loss of exon structures seen in WS115-WS116.

Corrected script for calculating confirmed_introns not in gene models. 

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 _____________