WormBase release WS132 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 WS132, Wormpep132 and Wormrna132 Fri Sep 24 11:28:35 BST 2004


WS132 was built by Anthony
======================================================================

This directory includes:
i)	database.WS132.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS132           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS132-WS131.dbcomp         -   log file reporting difference from last release
v)	wormpep132.tar.gz          -   full Wormpep distribution corresponding to WS132
vi)	wormrna132.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS132.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii)	cDNA2orf.WS132.gz            -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)	gene_interpolated_map_positions.WS132.gz    - Interpolated map positions for each coding/RNA gene
x)	clone_interpolated_map_positions.WS132.gz   - Interpolated map positions for each clone
xi)	best_blastp_hits.WS132.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.WS132.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii)	geneIDs.WS132.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)	PCR_product2gene.WS132.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 WS132
------------------------------------
brigdb : 2004-03-12
camace : 2004-09-13 - updated
citace : 2004-09-03 - updated
cshace : 2004-05-10
genace : 2004-09-13 - updated
stlace : 2004-09-11 - updated


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

       	WS132       	WS131      	change
----------------------------------------------
a    	32368573	32368573	  +0
c    	17781252	17781252	  +0
g    	17758265	17758265	  +0
t    	32369957	32369957	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100278047	100278047	  +0




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

There are 19726 CDS in autoace, 22288 when counting 2562 alternate splice forms.

The 22288 sequences contain 9,851,494 base pairs in total.

Modified entries             110
Deleted entries               89
New entries                   79
Reappeared entries             2


Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              5780 (25.9%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10940 (49.1%)	Some, but not all exon bases are covered by transcript evidence
Predicted              5568 (25.0%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2715 (12.2%)
TrEMBL accessions     19293 (86.6%)
TrEMBLnew accessions      0 (0.0%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22127 (99.3%)

CDS with GI_numbers   22093 (99.1%)


Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   5345


GeneModel correction progress WS131 -> WS132
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    441  |   -78  |
St Louis 	|    185  |   -24  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|    600  |    -4  |
St Louis 	|    775  |   -55  |
		+---------+--------+



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

No synchronisation issues


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



New Data:
---------
~4000 new OSTs from Vidal et al.

A recent effort in allele curation has doubled the number of alleles for which the molecular lesion is known.

New IPI_human dataset used for BLAST analysis.

The WormBase gene id system has been extended to include all C. briggsae genes.

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


Known Problems:
--------------
GFF files


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

Proposed Changes / Forthcoming Data:
------------------------------------
cyp - cyclophilin gene class will be renamed cyn and the cyp gene class will instead become cytochrome P450 ( ccp will be retired )
see CGC for more details.

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


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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