WormBase release WS136 now online

This is an automatic announcement that WormBase
(http://www.wormbase.org) has just been updated.  New releases occur
roughly every 2 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/

New release of WormBase WS136, Wormpep136 and Wormrna136 Fri Dec  3 16:07:46 GMT 2004


WS136 was built by Anthony
======================================================================

This directory includes:
i)	database.WS136.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS136           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS136-WS135.dbcomp         -   log file reporting difference from last release
v)	wormpep136.tar.gz          -   full Wormpep distribution corresponding to WS136
vi)	wormrna136.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS136.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii)	cDNA2orf.WS136.gz            -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)	gene_interpolated_map_positions.WS136.gz    - Interpolated map positions for each coding/RNA gene
x)	clone_interpolated_map_positions.WS136.gz   - Interpolated map positions for each clone
xi)	best_blastp_hits.WS136.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.WS136.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii)	geneIDs.WS136.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)	PCR_product2gene.WS136.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 WS136
------------------------------------
brigdb : 2004-03-12
camace : 2004-11-16 - updated
citace : 2004-11-12 - updated
cshace : 2004-10-14
genace : 2004-11-16 - updated
stlace : 2004-11-11 - updated


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

       	WS136       	WS135      	change
----------------------------------------------
a    	32368573	32368573	  +0
c    	17781252	17781252	  +0
g    	17758265	17758265	  +0
t    	32369957	32369957	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100278047	100278047	  +0




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

There are 19727 CDS in autoace, 22368 when counting 2641 alternate splice forms.

The 22368 sequences contain 9,922,374 base pairs in total.

Modified entries              42
Deleted entries               25
New entries                   48
Reappeared entries             7

Net change  +30



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              6261 (28.0%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11465 (51.3%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4642 (20.8%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2790 (12.5%)
TrEMBL accessions     19371 (86.6%)
TrEMBLnew accessions      0 (0.0%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22247 (99.5%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   5478


GeneModel correction progress WS135 -> WS136
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    370  |     0  |
St Louis 	|     42  |    -4  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|    588  |     2  |
St Louis 	|    777  |    16  |
		+---------+--------+



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

No synchronisation issues


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



New Data:
---------
BLASTP of C.elegans and C.briggsae protein sets against updated IPI_human proteins.

Update of alleles from the C.elegans Knockout Consortium


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


Known Problems:
--------------
BLASTX data from WS135 has been reused in this release due to technical problems re-running this.

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

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

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


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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