WormBase release WS165 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/WSWS165

New release of WormBase WS165, Wormpep165 and Wormrna165 Thu Sep 28 14:14:29 BST 2006


WS165 was built by Mary Ann
======================================================================

This directory includes:
i)   database.WS165.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS165           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS165-WS164.dbcomp         -   log file reporting difference from last release
v)   wormpep165.tar.gz          -   full Wormpep distribution corresponding to WS165
vi)   wormrna165.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS165.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS165.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS165.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS165.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS165.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.WS165.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS165.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS165.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:
----------------------------

       	WS165       	WS164      	change
----------------------------------------------
a    	32365888	32365888	  +0
c    	17779857	17779857	  +0
g    	17756012	17756012	  +0
t    	32365687	32365687	  +0
n    	0       	0       	  +0

Total	100267444	100267444	  +0


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


Gene data set (Live C.elegans genes 23819)
------------------------------------------
Molecular_info              22097 (92.8%)
Concise_description          4284 (18%)
Reference                    6357 (26.7%)
CGC_approved Gene name       8871 (37.2%)
RNAi_result                 19807 (83.2%)
Microarray_results          19129 (80.3%)
SAGE_transcript             19735 (82.9%)




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

There are 20080 CDS in autoace, 23192 when counting 3112 alternate splice forms.

The 23192 sequences contain 10,182,822 base pairs in total.

Modified entries              20
Deleted entries                4
New entries                   15
Reappeared entries             1

Net change  +12



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              7797 (33.6%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10753 (46.4%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4642 (20.0%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3270 (14.1%)
UniProtKB/TrEMBL accessions     19531 (84.2%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22801 (98.3%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   7203


GeneModel correction progress WS164 -> WS165
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     17  |    -2  |
St Louis 	|     10  |     0  |
		+---------+--------+


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:
---------
The #Molecular_change hash has been further populated with the following data:
Missense and Nonsense mutations - their location and details of the molecular lesion.
Splice sites - donor and acceptor sites and details of the molecular lesion.
Frameshift mutations.

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

None

New Fixes:
----------
A very long standing error with the C. briggsae genome sequence has been resolved.  
There were sequence objects mapped to cb25.fpc0022 that differ from the genomic sequences 
resulting in ambiguity in what the actual DNA sequence is.  The offending clones, 
listed below, have been removed.
c003000885.Contig2
c008401190.Contig3
c005101109.Contig1
c003000885.Contig2 

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

None

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

None.

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


Model Changes:
------------------------------------
Cloned_by tag has been added to ?Gene to allow us to curate when a laboratory other than 
that which owns the Gene_class clones the gene e.g. ?Gene Gene_info Cloned_by #Evidence

Laboratory_evidence tag has been added to ?Laboratory. e.g. ?Evidence Laboratory_evidence ?Laboratory

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


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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