WormBase release WS144 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 WS144, Wormpep144 and Wormrna144 Fri May 27 20:30:33 BST 2005


WS144 was built by Mary Ann
======================================================================

This directory includes:
i)   database.WS144.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS144           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS144-WS143.dbcomp         -   log file reporting difference from last release
v)   wormpep144.tar.gz          -   full Wormpep distribution corresponding to WS144
vi)   wormrna144.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS144.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS144.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS144.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS144.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS144.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.WS144.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS144.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS144.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 WS144
------------------------------------
brigdb : 2004-03-12
camace : 2005-05-09 - updated
citace : 2005-05-06 - updated
cshace : 2005-03-07
genace : 2005-05-09 - updated
stlace : 2005-05-06 - updated


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

       	WS144       	WS143      	change
----------------------------------------------
a    	32366710	32366710	  +0
c    	17780361	17780361	  +0
g    	17756435	17756435	  +0
t    	32366406	32366406	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100269912	100269912	  +0


Gene data set (Live C.elegans genes 23636)
------------------------------------------
Molecular_info              21826 (92.3%)
Concise_description          3985 (16.9%)
Reference                    4106 (17.4%)
CGC_approved Gene name       7706 (32.6%)
RNAi_result                 19760 (86.4%)
Microarray_results          18260 (77.3%)
SAGE_transcript             18313 (77.5%)




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

There are 19892 CDS in autoace, 22673 when counting 2781 alternate splice forms.

The 22673 sequences contain 10,025,551 base pairs in total.

Modified entries              39
Deleted entries               17
New entries                   59
Reappeared entries             5

Net change  +47



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              6434 (28.4%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11447 (50.5%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4792 (21.1%)	No transcriptional evidence at all



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            21020 (92.7%)


Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   6111


GeneModel correction progress WS143 -> WS144
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    121  |    -3  |
St Louis 	|     18  |   -14  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|    607  |    -6  |
St Louis 	|    838  |    -1  |
		+---------+--------+



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

No synchronisation issues


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

Model Changes
-------------

1) ?Variation and ?Gene have a new set of Status tags to indicate whether they are Live, 
Dead 
are 
Suppressed

 Status UNIQUE Live #Evidence
               Suppressed #Evidence
               Dead #Evidence


2) Tracking of members of Gene_class's is improved with a data previously stored in Remarks 
transfered in to specific tags in the Gene_class and Gene_name class


Gene_class
          Old_member ?Gene_name XREF Former_member_of

?Gene_name
          Former_member_of   ?Gene_class XREF Old_member // track old members of a class


New Data:
---------
uniprot-swissprot and uniprot-trembl BLASTP and BLASTX analyses have been updated to 
include versions 47 and 30 respectively

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.

____________  END _____________