WormBase release WS134 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 WS134, Wormpep134 and Wormrna134 Fri Oct 22 16:59:32 BST 2004


WS134 was built by Keith R. Bradnam
======================================================================

This directory includes:
i)	database.WS134.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS134           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS134-WS133.dbcomp         -   log file reporting difference from last release
v)	wormpep134.tar.gz          -   full Wormpep distribution corresponding to WS134
vi)	wormrna134.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS134.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii)	cDNA2orf.WS134.gz            -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)	gene_interpolated_map_positions.WS134.gz    - Interpolated map positions for each coding/RNA gene
x)	clone_interpolated_map_positions.WS134.gz   - Interpolated map positions for each clone
xi)	best_blastp_hits.WS134.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.WS134.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii)	geneIDs.WS134.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)	PCR_product2gene.WS134.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 WS134
------------------------------------
brigdb : 2004-03-12
camace : 2004-10-11 - updated
citace : 2004-10-08 - updated
cshace : 2004-05-10
genace : 2004-10-11 - updated
stlace : 2004-10-10 - updated


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

       	WS134       	WS133      	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 19720 CDS in autoace, 22321 when counting 2601 alternate splice forms.

The 22321 sequences contain 9,887,637 base pairs in total.

Modified entries              51
Deleted entries               25
New entries                   47
Reappeared entries             2

Net change  +24



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              6222 (27.9%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11461 (51.3%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4638 (20.8%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2737 (12.3%)
TrEMBL accessions     19296 (86.4%)
TrEMBLnew accessions      0 (0.0%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22192 (99.4%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   5438


GeneModel correction progress WS133 -> WS134
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    370  |    -8  |
St Louis 	|     52  |   -18  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|    594  |    -1  |
St Louis 	|    776  |     0  |
		+---------+--------+



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:
----------


Known Problems:
--------------


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

Proposed Changes / Forthcoming Data:
------------------------------------
A set of binding site features curated from the literature will be added to the next release.

New data in the form of gene interaction data will be included.

RNAi objects are all being renamed to anonymous identifiers (e.g. WBRNAi0001023) as current RNAi
objects are named after sequence or CGC names of genes, both of which can change (thus the RNAi
object name becomes misleading).  The current names will be stored.

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


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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