WormBase release WS129 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 WS129, Wormpep129 and Wormrna129 Fri Jul 30 2004


WS129 was built by me
======================================================================

This directory includes:
i)	database.WS129.*.tar.gz                     -   compressed data for new release
ii)	models.wrm.WS129                            -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir                          -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS129-WS128.dbcomp                          -   log file reporting difference from last release
v)	wormpep129.tar.gz                           -   full Wormpep distribution corresponding to WS129
vi)	wormrna129.tar.gz                           -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS129.gz                    -   DNA sequences of all genes confirmed by EST &/or cDNA
viii)	yk2orf.WS129.gz                             -    Latest set of ORF connections to each Yuji Kohara EST clone
ix)	gene_interpolated_map_positions.WS129.gz    - Interpolated map positions for each coding/RNA gene
x)	clone_interpolated_map_positions.WS129.gz   - Interpolated map positions for each clone
xi)	best_blastp_hits.WS129.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.WS129.gz          - for each C. briggsae protein, lists Best blastp match to
                                                      human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii)	geneIDs.WS129.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 WS129
------------------------------------
brigdb : 2004-03-12
camace : 2004-07-20 - updated
citace : 2004-07-15 - updated
cshace : 2004-05-10
genace : 2004-07-22 - updated
stlace : 2004-07-19 - updated


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

       	WS129       	WS128      	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 19763 CDS in autoace, 22213 when counting 2450 alternate splice forms.

The 22213 sequences contain 9,802,206 base pairs in total.

Modified entries              50
Deleted entries               59
New entries                   95
Reappeared entries             3

Net change  +39


Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              5536 (24.9%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10892 (49.0%)	Some, but not all exon bases are covered by transcript evidence
Predicted              5785 (26.0%)	No transcriptional evidence at all


Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2651 (11.9%)
TrEMBL accessions     19281 (86.8%)
TrEMBLnew accessions      0 (0.0%)


Status of entries: Connections in public nucleotide databases
-------------------------------------------------------------
Protein_id            22030 (99.2%)
GI_number             21987 (99.0%)

Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   5194

Functional data associated with Genes
-------------------------------------

Gene with non-WT RNAi phenotype    7022
Gene with microarray_result       18448


GeneModel correction progress WS128 -> WS129
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    571  |   -45  |
St Louis 	|    367  |   -79  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|    620  |     2  |
St Louis 	|    872  |    -1  |
		+---------+--------+



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

CHROMOSOME_II	sequence U39471

There are no gaps remaining in the genome sequence

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



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

Microarray_result data is better linked to the Gene/CDS/Transcript and Pseudogene classes
as part of the build procedure.

Yeast2Hybrid data from the Interactome is dynamically mapped to Gene/CDS/Transcript and
pseudogene classes for the first time. 

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

Tidy up of GI number connections to remove old redundant data.

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


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

Proposed Changes / Forthcoming Data:
------------------------------------

Gene spans have been included in the GFF files for the past two releases. We will be adding these
into the database proper for WS130. This will help in streamlining some of the dynamic mappings
which happen during the build to connect data to gene models (e.g. the coordinates for operons, 
Overlapping genes for functional data such as expression microarrays or RNAi).

Features will be linked to Genes/CDS/Transcripts in WS130 as part of the ongoing improvement 
in gene prediction and accomodating TSL/polyA data into the prediction of full-length
transcript models.

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


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.

____________  END _____________