WormBase release WS137 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/

x1New release of WormBase WS137, Wormpep137 and Wormrna137  23rd Dec 2004


WS137 was built by me
======================================================================

This directory includes:
i)	database.WS137.*.tar.gz                    - compressed data for new release
ii)	models.wrm.WS137                           - the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir                         - contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS137-WS136.dbcomp                         - log file reporting difference from last release
v)	wormpep137.tar.gz                          - full Wormpep distribution corresponding to WS137
vi)	wormrna137.tar.gz                          - latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS137.gz                   - DNA sequences of all genes confirmed by EST &/or cDNA
viii)	cDNA2orf.WS137.gz                          - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)	gene_interpolated_map_positions.WS137.gz   - Interpolated map positions for each coding/RNA gene
x)	clone_interpolated_map_positions.WS137.gz  - Interpolated map positions for each clone
xi)	best_blastp_hits.WS137.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.WS137.gz         - for each C. briggsae protein, lists Best blastp match to
                                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii)	geneIDs.WS137.gz                           - list of all current gene identifiers with CGC & molecular names (when known)
xiv)	PCR_product2gene.WS137.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 WS137
------------------------------------
brigdb : 2004-03-12
camace : 2004-12-07 - updated
citace : 2004-12-05 - updated
cshace : 2004-10-14
genace : 2004-12-06 - updated
stlace : 2004-12-02 - updated


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

       	WS137       	WS136      	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


Gene data set (Live C.elegans genes 23376)
------------------------------------------
Molecular_info              21516 (92.0%)
Concise_description          3789 (16.2%)
Reference                    3955 (16.9%)
CGC_approved Gene name       5558 (23.8%)
RNAi_result                 16494 (70.6%)
Microarray_results          18213 (77.9%)
SAGE_transcript             18304 (78.3%)


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

There are 19730 CDS in autoace, 22382 when counting 2652 alternate splice forms.

The 22382 sequences contain 9,928,144 base pairs in total.

Modified entries              37
Deleted entries               24
New entries                   37
Reappeared entries             1

Net change  +14



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              6285 (28.1%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11453 (51.2%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4644 (20.7%)	No transcriptional evidence at all


Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2794 (12.5%)
TrEMBL accessions     19339 (86.4%)
TrEMBLnew accessions      0 ( 0.0%)


Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22187 (99.1%)
GI_number             21980 (98.2%)


GeneModel correction progress WS136 -> WS137
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    336  |   -34  |
St Louis 	|     39  |    -3  |
		+---------+--------+

Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|    583  |    -5  |
St Louis 	|    777  |     0  |
		+---------+--------+



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

CHROMOSOME_II	sequence Z83108

There are no gaps remaining in the genome sequence


For more info mail [email protected]
-===================================================================================-



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

RNAi experiments are now mapped via a Homol rather than SMap. This will allow us to 
show multiple-hits within the genome, and experiments which use multiple RNAs to
knocksown two or more genes at the same time.

Updates of the Human IPI and Flybase proteome sets.

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

Interaction data makes connections to the WBGene nomenclature

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


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

Expanded Gene data statistics in the release notes (this file)

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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