WormBase release WS152 now online

This is an automatic announcement that WormBase
(http://www.wormbase.org) has just been updated.  New releases occur
roughly every three 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/
   or
   ftp://ftp.wormbase.org/pub/wormbase/elegans/current_release

New release of WormBase WS152, Wormpep152 and Wormrna152 Mon Dec 19 11:54:06 GMT 2005


WS152 was built by Michael
======================================================================

This directory includes:
i)   database.WS152.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS152           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS152-WS151.dbcomp         -   log file reporting difference from last release
v)   wormpep152.tar.gz          -   full Wormpep distribution corresponding to WS152
vi)   wormrna152.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS152.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS152.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS152.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS152.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS152.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.WS152.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS152.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS152.gz   - Mappings between PCR products and overlapping Genes


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



Primary databases used in build WS152
------------------------------------
brigdb : 2004-03-12
camace : 2005-11-28 - updated
citace : 2005-11-22 - updated
cshace : 2005-11-04
genace : 2005-11-28 - updated
stlace : 2005-11-23 - updated


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

       	WS152       	WS151      	change
----------------------------------------------
a    	32366710	32366710	  +0
c    	17780365	17780365	  +0
g    	17756436	17756436	  +0
t    	32366406	32366406	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100269917	100269917	  +0


Gene data set (Live C.elegans genes 23688)
------------------------------------------
Molecular_info              21934 (92.6%)
Concise_description          4120 (17.4%)
Reference                    4854 (20.5%)
CGC_approved Gene name       8375 (35.4%)
RNAi_result                 19783 (83.5%)
Microarray_results          19145 (80.8%)
SAGE_transcript             18213 (76.9%)




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

There are 20066 CDS in autoace, 22901 when counting 2835 alternate splice forms.

The 22901 sequences contain 10,068,096 base pairs in total.

Modified entries             107
Deleted entries               43
New entries                   58
Reappeared entries             5

Net change  +20



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              6555 (28.6%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11402 (49.8%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4944 (21.6%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3101 (13.5%)
UniProtKB/TrEMBL accessions     19518 (85.2%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22619 (98.8%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   6684


GeneModel correction progress WS151 -> WS152
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    148  |  -102  |
St Louis 	|      7  |    -1  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|    590  |   169  |
St Louis 	|    766  |   117  |
		+---------+--------+



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

No synchronisation issues


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



New Data:
---------
~3.500 new TEC-Red data from Paul Sternberg's lab.
interpolated genetic map positions for SNPs
updated yeast homology data from SGD

New Fixes:
----------
fixed redundancy from nematode EST clusters.
fixed oligo mapping issues

Known Problems:
--------------
none

Other Changes:
--------------
none

Proposed Changes / Forthcoming Data:
------------------------------------
improved handling of URLs
refinement of the genomic sequence
extension of the Variation annotation

Model Changes:
------------------------------------
?phenotype has been reverted to WS149 in agreement with Carol.  New tags though agreed were not meant to be entered yet.
?Database class overhauled in prep. for URL construction
Another status tag added to Structure_data
Feature added to #Evidence 

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


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 _____________