WormBase release WS157 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/WSWS157

New release of WormBase WS157, Wormpep157 and Wormrna157 Thu Apr 13 17:41:54 BST 2006


WS157 was built by [INSERT NAME HERE]
======================================================================

This directory includes:
i)   database.WS157.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS157           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS157-WS156.dbcomp         -   log file reporting difference from last release
v)   wormpep157.tar.gz          -   full Wormpep distribution corresponding to WS157
vi)   wormrna157.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS157.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS157.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS157.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS157.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS157.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.WS157.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS157.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS157.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:
----------------------------

       	WS157       	WS156      	change
----------------------------------------------
a    	32365775	32365775	  +0
c    	17779813	17779813	  +0
g    	17755968	17755968	  +0
t    	32365578	32365578	  +0
n    	0       	0       	  +0

Total	100267134	100267134	  +0


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


Gene data set (Live C.elegans genes 23756)
------------------------------------------
Molecular_info              22009 (92.6%)
Concise_description          4135 (17.4%)
Reference                    5014 (21.1%)
CGC_approved Gene name       8755 (36.9%)
RNAi_result                 19796 (83.3%)
Microarray_results          19116 (80.5%)
SAGE_transcript             18188 (76.6%)




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

There are 20102 CDS in autoace, 23162 when counting 3060 alternate splice forms.

The 23162 sequences contain 10,162,616 base pairs in total.

Modified entries             102
Deleted entries               52
New entries                  125
Reappeared entries             3

Net change  +76



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              6681 (28.8%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11445 (49.4%)	Some, but not all exon bases are covered by transcript evidence
Predicted              5036 (21.7%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3192 (13.8%)
UniProtKB/TrEMBL accessions     19608 (84.7%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22800 (98.4%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   7068


GeneModel correction progress WS156 -> WS157
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|   3250  |  3151  |  *this is wrong !
St Louis 	|     17  |     9  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|    579  |    -1  |
St Louis 	|    749  |    -1  |
		+---------+--------+



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

No synchronisation issues


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



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

# REACTOME links
# 8 additional microarray datasets
# updated SGD and FlyBase data
# added interpolated map position to all alleles with sequence info (not just SNPs)


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


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


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

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


Model Changes:
------------------------------------
#  Variation has an added Deletion_verification tag for tracking conformation test carried out by the KO Consortium
#  Microarray_data has changed the frequency from Int to float

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


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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