WormBase release WS100 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 acedb WS100, Wormpep100 and Wormrna100 Fri May  2 13:50:03 BST 2003

WS100 was built by Dan Lawson (and a little bit by Keith Bradnam)
======================================================================

This directory includes:
i)	database.WS100.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS100           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir        -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS100-WS99.dbcomp          -   log file reporting difference from last release
v)	wormpep100.tar.gz          -   full Wormpep distribution corresponding to WS100
vi)	wormrna100.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS100.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA


Release notes on the web:
-------------------------
http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE



Primary databases used in build WS100
------------------------------------
brigdb : 2003-04-18 - updated
camace : 2003-04-23 - updated
citace : 2003-04-22 - updated
cshace : 2003-04-12 - updated
genace : 2003-04-30 - updated
stlace : 2003-04-18 - updated


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

       	WS100       	WS99      	change
----------------------------------------------
a    	32364258	32364259	  -1
c    	17778488	17778485	  +3
g    	17755882	17755881	  +1
t    	32365362	32365361	  +1
n    	95      	95      	  +0
-    	0       	0       	  +0

Total	100264085	100264081	  +4




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

There are 19560 CDS in autoace, 21565 when counting 2002 alternate splice forms.

The 21565 sequences contain 9,494,869 base pairs in total.

Modified entries              96
Deleted entries               45
New entries                   95
Reappeared entries             4

Net change  +54



Status of entries: Confidence level of prediction
-------------------------------------------------
Confirmed              3889 (18.0%)
Partially_confirmed    8848 (41.0%)
Predicted              8828 (40.9%)



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2287 (10.6%)
TrEMBL accessions     18364 (85.2%)
TrEMBLnew accessions    903 (4.2%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            21554 (99.9%)



Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection   3965


GeneModel correction progress WS99 -> WS100
-----------------------------------------
Confirmed introns not is a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|   1099  |   504  |
St Louis 	|   1274  |  1155  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     25  |     0  |
St Louis 	|     24  |     0  |
		+---------+--------+



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

CHROMOSOME_I	sequence Z78420
CHROMOSOME_I	sequence Z81587
CHROMOSOME_II	sequence Z68318
CHROMOSOME_II	sequence AL110484
CHROMOSOME_II	sequence Z93393
CHROMOSOME_V	sequence Z70780

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



New Data:
---------
New ?GO_code class.  All use of GO terms in database are now followed by a three-letter 
GO code (IEA, IMP etc.)

New Orfeome data has produced many more confirmed introns. 

Orfeome OST tags are now handled using separate database methods (BLAT_OST_BEST and
BLAT_OST_OTHER) and therefore will be available as separate tracks on the 'Genome Browser'
on the WormBase website.

Some updates to operon data.

Brigpep (set of C. briggsae peptides), now searched against Pfam domains and also now
shows best matches to C. elegans proteins (Wormpep).

Many alleles have had expanded information added to properly describe the sequence difference
in the allele.  This is ongoing work, but this approach allows to accurately map allele
positions each build (should genome sequence change).


New Fixes:
----------
A number of corrections have been made to the genome sequence (based on analysis of transcript
data by Danielle et Jean Thierry-Mieg).  This has led to a small change in the total genome
size (see section above).

Orfeome PCR products have a new database Method.

C. briggsae RNA genes now in ?Transcript class.

Much work done in trying to remove bad 'Matching_cDNA' tags that had incorrectly connected 
predicted genes to cDNA sequences.

New methods for Alleles to hopefully allow all alleles (not just Knockout consortium alleles)
to be displayed in an 'Allele' track on the 'Genome Browser' part of WormBase.


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


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


Proposed Changes / Forthcoming Data:
------------------------------------
All use of accession evidence to be standardised to include database names (EMBL, GenBank, RefSeq etc.)

Changes to ?Feature model

Hopefully incoroporate revised and updated interpolated genetic map, with each CDS (predicted gene)
getting an interpolated genetic map position.

Big tidy up of database schema to remove many unused tags.


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


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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