WormBase release WS143 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 WS143, Wormpep143 and Wormrna143 Fri May  6 10:18:57 BST 2005


WS143 was built by Thursday
======================================================================

This directory includes:
i)   database.WS143.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS143           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS143-WS142.dbcomp         -   log file reporting difference from last release
v)   wormpep143.tar.gz          -   full Wormpep distribution corresponding to WS143
vi)   wormrna143.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS143.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS143.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS143.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS143.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS143.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.WS143.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS143.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS143.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 WS143
------------------------------------
brigdb : 2004-03-12
camace : 2005-04-18 - updated
citace : 2005-04-16 - updated
cshace : 2005-03-07
genace : 2005-04-18 - updated
stlace : 2005-04-14 - updated


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

       	WS143       	WS142      	change
----------------------------------------------
a    	32366710	32366710	  +0
c    	17780361	17780361	  +0
g    	17756435	17756435	  +0
t    	32366406	32366406	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100269912	100269912	  +0


Gene data set (Live C.elegans genes 23636)
------------------------------------------
Molecular_info              21826 (92.3%)
Concise_description          3985 (16.9%)
Reference                    4106 (17.4%)
CGC_approved Gene name       7706 (32.6%)
RNAi_result                 19631 (83.1%)
Microarray_results          18260 (77.3%)
SAGE_transcript             18313 (77.5%)




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

There are 19854 CDS in autoace, 22626 when counting 2772 alternate splice forms.

The 22626 sequences contain 10,007,360 base pairs in total.

Modified entries              62
Deleted entries               50
New entries                   59
Reappeared entries             9

Net change  +18



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              6427 (28.4%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11445 (50.6%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4754 (21.0%)	No transcriptional evidence at all


Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22555 (99.7%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   5965


GeneModel correction progress WS142 -> WS143
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    124  |   -54  |
St Louis 	|     32  |     2  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|    613  |     0  |
St Louis 	|    839  |    -8  |
		+---------+--------+



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

No synchronisation issues


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



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


New Fixes:
----------
Fixed problem getting protein_ids from EBI



Known Problems:
--------------
3 clones are missing some CDS's in GenBank/EMBL/DDBJ entries - C55A1, F25H5, W09C2


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.

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