WormBase release WS162 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/WSWS162

New release of WormBase WS162, Wormpep162 and Wormrna162 Thu Jul 27 09:59:43 BST 2006


WS162 was built by [mh6]
======================================================================

This directory includes:
i)   database.WS162.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS162           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS162-WS161.dbcomp         -   log file reporting difference from last release
v)   wormpep162.tar.gz          -   full Wormpep distribution corresponding to WS162
vi)   wormrna162.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS162.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS162.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS162.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS162.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS162.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.WS162.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS162.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS162.gz   - Mappings between PCR products and overlapping Genes


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


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

       	WS162       	WS161      	change
----------------------------------------------
a    	32365888	32365888	  +0
c    	17779855	17779855	  +0
g    	17756011	17756011	  +0
t    	32365687	32365687	  +0
n    	0       	0       	  +0

Total	100267441	100267441	  +0


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


Gene data set (Live C.elegans genes 23750)
------------------------------------------
Molecular_info              22025 (92.7%)
Concise_description          4204 (17.7%)
Reference                    6279 (26.4%)
CGC_approved Gene name       8819 (37.1%)
RNAi_result                 19799 (83.4%)
Microarray_results          19120 (80.5%)
SAGE_transcript             18158 (76.5%)




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

There are 20069 CDS in autoace, 23155 when counting 3086 alternate splice forms.

The 23155 sequences contain 10,167,337 base pairs in total.

Modified entries              13
Deleted entries                5
New entries                   12
Reappeared entries             0

Net change  +7



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              7760 (33.5%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10752 (46.4%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4643 (20.1%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3255 (14.1%)
UniProtKB/TrEMBL accessions     19617 (84.7%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22872 (98.8%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   7153


GeneModel correction progress WS161 -> WS162
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     17  |     1  |
St Louis 	|      5  |     0  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|    569  |     0  |
St Louis 	|    746  |    -1  |
		+---------+--------+



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

No synchronisation issues


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

Changes:
--------------
new supplementary GFF files added to the release for data not available in Acedb, 
but of potential interest like predicted micro-RNA binding sites and alternative
gene predictions.

This will be used to display predicted data that has not been experimentally proven.  
If you would like to submit such data please email [email protected] 


Proposed Changes / Forthcoming Data for WS163:
-----------------------------------------------
There will be an overhaul of the SAGE data structures to make this data more accessible. 
Small changes to the genomical sequences from the latest sequence curations.

Model Changes:
------------------------------------
There were no database model changes for WS162


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


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 _____________