WormBase release WS140 now online

This is an automatic announcement that WormBase
(http://www.wormbase.org) has just been updated.  New releases occur
roughly every three 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/
   or
   ftp://ftp.wormbase.org/pub/wormbase/elegans/current_release

New release of WormBase WS140, Wormpep140 and Wormrna140 Fri Mar  4 12:02:35 GMT 2005


WS140 was built by Dan & Mary Ann
======================================================================

This directory includes:
i)	database.WS140.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS140           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS140-WS139.dbcomp         -   log file reporting difference from last release
v)	wormpep140.tar.gz          -   full Wormpep distribution corresponding to WS140
vi)	wormrna140.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS140.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii)	cDNA2orf.WS140.gz            -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)	gene_interpolated_map_positions.WS140.gz    - Interpolated map positions for each coding/RNA gene
x)	clone_interpolated_map_positions.WS140.gz   - Interpolated map positions for each clone
xi)	best_blastp_hits.WS140.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.WS140.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii)	geneIDs.WS140.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)	PCR_product2gene.WS140.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 WS140
------------------------------------
brigdb : 2004-03-12
camace : 2005-02-15 - updated
citace : 2005-02-11 - updated
cshace : 2005-01-30 - updated
genace : 2005-02-14 - updated
stlace : 2005-02-11 - updated


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

       	WS140       	WS139      	change
----------------------------------------------
a    	32368572	32368573	  -1
c    	17781252	17781252	  +0
g    	17758265	17758265	  +0
t    	32369957	32369957	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100278046	100278047	  -1


Gene data set (Live C.elegans genes 23434)
------------------------------------------
Molecular_info              21643 (92.2%)
Concise_description          3870 (16.5%)
Reference                    4036 (17.2%)
CGC_approved Gene name       7555 (32.2%)
RNAi_result                 16515 (70.4%)
Microarray_results          18234 (77.7%)
SAGE_transcript             18314 (78.0%)



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

There are 19735 CDS in autoace, 22420 when counting 2685 alternate splice forms.

The 22420 sequences contain 9,949,630 base pairs in total.

Modified entries              84
Deleted entries               51
New entries                   54
Reappeared entries             7

Net change  +10



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              6332 (28.2%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11435 (51.0%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4653 (20.8%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions  21424 (95.6%)
TrEMBL accessions         4 (0.0%)
TrEMBLnew accessions      0 (0.0%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            21536 (96.1%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   5813


GeneModel correction progress WS139 -> WS140
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    261  |    -8  |
St Louis 	|     36  |     0  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|    579  |    -1  |
St Louis 	|    770  |    -5  |
		+---------+--------+



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

No synchronisation issues


There are no gaps remaining in the genome sequence
---------------

For more info mail [email protected]

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



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

Variation class replaces Allele and part of Locus. 

Vidal lab promoterome data added. New Oligo and PCR_product objects.


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

Fewer Coding_transcript objects as more 

TSL leader mappings expanded to include 3' ESTs

Transmembrane domains for protein objects return after a lengthy absence.

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



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


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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