WormBase release WS105 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 WS105, Wormpep105 and Wormrna105 Fri Jul 11 12:31:21 BST 2003


WS105 was built by Chao-Kung Chen ([email protected])
======================================================================

This directory includes:
i)	database.WS105.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS105           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir        -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS105-WS104.dbcomp          -   log file reporting difference from last release
v)	wormpep105.tar.gz          -   full Wormpep distribution corresponding to WS105
vi)	wormrna105.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS105.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 WS105
------------------------------------
brigdb : 2003-06-14
camace : 2003-06-30 - updated
citace : 2003-06-27 - updated
cshace : 2003-06-16 - updated
genace : 2003-06-30 - updated
stlace : 2003-06-14


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

       	WS105       	WS104      	change
----------------------------------------------
a    	32367166	32367166	  +0
c    	17780238	17780238	  +0
g    	17757588	17757588	  +0
t    	32368415	32368415	  +0
n    	95      	95      	  +0
-    	0       	0       	  +0

Total	100273502	100273502	  +0




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

There are 19569 CDS in autoace, 21699 when counting 2126 alternate splice forms.

The 21699 sequences contain  base pairs in total.

Modified entries              28
Deleted entries               36
New entries                   23
Reappeared entries             0

Net change  -13The differnce between the total CDS's of this (21699) and the last build () does not equal the net change -13
Please investigate! ! 




Status of entries: Confidence level of prediction
-------------------------------------------------
Confirmed              4467 (20.6%)
Partially_confirmed    8645 (39.9%)
Predicted              8575 (39.5%)



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2376 (11.0%)
TrEMBL accessions     18682 (86.1%)
TrEMBLnew accessions    602 (2.8%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            21664 (99.9%)



Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection   4391


GeneModel correction progress WS104 -> WS105
-----------------------------------------
Confirmed introns not is a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|   1212  |   -24  |
St Louis 	|   1235  |     5  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     25  |    -1  |
St Louis 	|     28  |     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:
---------
Interpolated map positions for CDSes and Clone in two files:
WS105_CDSes_interpolated_map.txt.gz
WS105_Clones_interpolated_map.txt.gz

You can download them from 
ftp://ftp.sanger.ac.uk/pub/wormbase

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

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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