WormBase release WS126 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 WS126, Wormpep126 and Wormrna126 Fri Jun 18 13:06:00 BST 2004


WS126 was built by Keith Bradnam
======================================================================

This directory includes:
i)	database.WS126.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS126           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS126-WS125.dbcomp         -   log file reporting difference from last release
v)	wormpep126.tar.gz          -   full Wormpep distribution corresponding to WS126
vi)	wormrna126.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS126.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii)	yk2orf.WS126.gz            -    Latest set of ORF connections to each Yuji Kohara EST clone
ix)	gene_interpolated_map_positions.WS126.gz    - Interpolated map positions for each coding/RNA gene
x)	clone_interpolated_map_positions.WS126.gz    - Interpolated map positions for each clone
xi)	best_blastp_hits.WS126.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.WS126.gz   - for each C. briggsae protein, lists Best blastp match to
 
                                        human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii)	geneIDs.WS126.gz   - list of all current gene identifiers with CGC & molecular names (when known)


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



Primary databases used in build WS126
------------------------------------
brigdb : 2004-03-12
camace : 2004-05-28 - updated
citace : 2004-05-26 - updated
cshace : 2004-05-10 - updated
genace : 2004-06-03 - updated
stlace : 2004-05-26 - updated


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

       	WS126       	WS125      	change
----------------------------------------------
a    	32368574	32368570	  +4
c    	17781251	17781251	  +0
g    	17758269	17758269	  +0
t    	32369958	32369957	  +1
n    	1       	6       	  -5
-    	0       	0       	  +0

Total	100278053	100278053	  +0




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

There are 19856 CDS in autoace, 22228 when counting 2372 alternate splice forms.

The 22228 sequences contain 9,818,626 base pairs in total.

Modified entries              84
Deleted entries               25
New entries                   19
Reappeared entries             5

Net change  -1



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              5486 (24.7%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11399 (51.3%)	Some, but not all exon bases are covered by transcript evidence
Predicted              5343 (24.0%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2587 (11.6%)
TrEMBL accessions     18496 (83.2%)
TrEMBLnew accessions    887 (4.0%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            21974 (98.9%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   5142


GeneModel correction progress WS125 -> WS126
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    746  |    67  |
St Louis 	|    606  |   103  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|    679  |    -1  |
St Louis 	|    989  |   -58  |
		+---------+--------+



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

CHROMOSOME_II	sequence U39471
CHROMOSOME_II	sequence Z46676

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



New Data:
---------
WormBase Gene IDs have now been assigned for all genes in the genome (either genes defined
genetically or at the molecular level).  These identifiers take the form WBGene00000001 and
will remain even when corresponding gene predictions are removed.

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


Known Problems:
--------------
A small number of non-coding RNA genes were lost in this build...they should return for WS127

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

Proposed Changes / Forthcoming Data:
------------------------------------
In WS127 (or possibly WS128) we will be refining our UTR data.  UTRs will extend to splice leader 
sequences (where known) at the 5' end and to the polyA site (where known) at the 3' end.  In addition
we will be detailing new isoforms of genes which differ only in the UTR region.

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


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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