WormBase release WS148 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/acedb/current_release

New release of WormBase WS148, Wormpep148 and Wormrna148 Fri Sep  9 09:20:07 BST 2005


WS148 was built by Anthony
======================================================================

This directory includes:
i)   database.WS148.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS148           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS148-WS147.dbcomp         -   log file reporting difference from last release
v)   wormpep148.tar.gz          -   full Wormpep distribution corresponding to WS148
vi)   wormrna148.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS148.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS148.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS148.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS148.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS148.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.WS148.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS148.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS148.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 WS148
------------------------------------
brigdb : 2004-03-12
camace : 2005-08-23 - updated
citace : 2005-08-19 - updated
cshace : 2005-03-07
genace : 2005-08-23 - updated
stlace : 2005-08-19 - updated


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

       	WS148       	WS147      	change
----------------------------------------------
a    	32366710	32366710	  +0
c    	17780361	17780361	  +0
g    	17756436	17756436	  +0
t    	32366406	32366406	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100269913	100269913	  +0


Gene data set (Live C.elegans genes 23919)
------------------------------------------
Molecular_info              22113 (92.4%)
Concise_description          4095 (17.1%)
Reference                    4665 (19.5%)
CGC_approved Gene name       8272 (34.6%)
RNAi_result                 19661 (82.2%)
Microarray_results          19118 (79.9%)
SAGE_transcript             18298 (76.5%)




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

There are 20061 CDS in autoace, 22829 when counting 2768 alternate splice forms.

The 22829 sequences contain 10,033,251 base pairs in total.

Modified entries              67
Deleted entries               12
New entries                   35
Reappeared entries             0

Net change  +23



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              6458 (28.3%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11420 (50.0%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4951 (21.7%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   2948 (12.9%)
UniProtKB/TrEMBL accessions     19512 (85.5%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22460 (98.4%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   6532


GeneModel correction progress WS147 -> WS148
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    138  |   -48  |
St Louis 	|     22  |   -60  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|    593  |     0  |
St Louis 	|    788  |    -6  |
		+---------+--------+



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

No synchronisation issues


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



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


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


Known Problems:
--------------
Homol alignments have historically been stored incorrectly, using the Align tag for all molecule types.
Alignments between Proteins and DNA should use the AlignPepDNA tag instead.  This will be fixed for a future release.


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

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


Model Changes:
------------------------------------
?Cluster replaced by ?Expression_cluster

?Variation class has had several Phenotype description tags reinstated.

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


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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