WormBase release WS175 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

Additional information on the release, including any necessary patches or bug
fixes can be found on the WormBaseWiki:

   http://www.wormbase.org/wiki/index.php/WSWS175

New release of WormBase WS175, Wormpep175 and Wormrna175 Fri May  4 16:29:43 BST 2007


WS175 was built by [Anthony]
======================================================================

This directory includes:
i)   database.WS175.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS175           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS175-WS174.dbcomp         -   log file reporting difference from last release
v)   wormpep175.tar.gz          -   full Wormpep distribution corresponding to WS175
vi)   wormrna175.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS175.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS175.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS175.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS175.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS175.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.WS175.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS175.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS175.gz   - Mappings between PCR products and overlapping Genes


Release notes on the web:
-------------------------
http://www.wormbase.org/wiki/index.php/Release_notes



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

       	WS175       	WS174      	change
----------------------------------------------
a    	32365889	32365889	  +0
c    	17779856	17779856	  +0
g    	17756016	17756016	  +0
t    	32365689	32365689	  +0
n    	0       	0       	  +0

Total	100267450	100267450	  +0


Chromosomal Changes:
--------------------
There are no changes to the chromosome sequences in this release.


Gene data set (Live C.elegans genes 24085)
------------------------------------------
Molecular_info              22393 (93%)
Concise_description          4579 (19%)
Reference                    7004 (29.1%)
CGC_approved Gene name       9177 (38.1%)
RNAi_result                 19871 (82.5%)
Microarray_results          19149 (79.5%)
SAGE_transcript             20043 (83.2%)




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

There are 20115 CDS in autoace, 23273 when counting 3158 alternate splice forms.

The 23273 sequences contain 10,219,495 base pairs in total.

Modified entries              42
Deleted entries                8
New entries                   21
Reappeared entries             2

Net change  +15



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              7866 (33.8%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10792 (46.4%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4615 (19.8%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3496 (15.0%)
UniProtKB/TrEMBL accessions     19225 (82.6%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22694 (97.5%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   7537


GeneModel correction progress WS174 -> WS175
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    173  |   -13  |
St Louis 	|    212  |    -3  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|      6  |     0  |
St Louis 	|      6  |     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:
---------
Database cross references to miRBase have been added to 131 genes. 

Genome sequence updates:
-----------------------


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


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


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

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


Model Changes:
------------------------------------
Added tags to ?Person and ?Paper to enable recording of negative connections ie Mr X did NOT contribue to this paper.

Added Map_evidence to ?Transgene so that the paper that mapping data is taken from can be attributed

Added a tags to ?Expr_pattern and  ?Expression_cluster to handle Localizome data

Changes in the ?Interaction model as proposed by Andrei.  Added #Interactor_info and #Interaction_info

Directed_Y1H in YH class

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


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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