WormBase release WS145 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/elegans/current_release

New release of WormBase WS145, Wormpep145 and Wormrna145 2005-06-17

WS145 was built by D
======================================================================

This directory includes:
i)    database.WS145.*.tar.gz                     - compressed data for new release
ii)   models.wrm.WS145                            - the latest database schema (also in above database files)
iii)  CHROMOSOMES/subdir                          - contains 3 files (DNA, GFF & AGP per chromosome)
iv)   WS145-WS144.dbcomp                          - log file reporting difference from last release
v)    wormpep145.tar.gz                           - full Wormpep distribution corresponding to WS145
vi)   wormrna145.tar.gz                           - latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS145.gz                    - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS145.gz                           - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS145.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS145.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS145.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.WS145.gz          - for each C. briggsae protein, lists Best blastp match to
                                                    human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS145.gz                            - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS145.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 WS145
------------------------------------
brigdb : 2004-03-12
camace : 2005-05-31 - updated
citace : 2005-05-29 - updated
cshace : 2005-03-07
genace : 2005-06-01 - updated
stlace : 2005-05-26 - updated


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

       	WS145       	WS144      	change
----------------------------------------------
a    	32366710	32366710	  +0
c    	17780361	17780361	  +0
g    	17756435	17756435	  +0
t    	32366406	32366406	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100269912	100269912	  +0


Gene data set (Live C.elegans genes 23774)
------------------------------------------
Molecular_info              21955 (92.3%)
Concise_description          3995 (16.8%)
Reference                    4131 (17.4%)
CGC_approved Gene name       7882 (33.2%)
RNAi_result                 19801 (83.3%)
Microarray_results          18279 (76.9%)
SAGE_transcript             18306 (77.0%)



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

There are 19971 CDS in autoace, 22730 when counting 2759 alternate splice forms.

The 22730 sequences contain 10,028,624 base pairs in total.

Modified entries              11
Deleted entries               42
New entries                   87
Reappeared entries            12

Net change  +57



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              6436 (28.3%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11436 (50.3%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4858 (21.4%)	No transcriptional evidence at all


Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions  22305 (98.1%)
TrEMBL accessions         4 (0.0%)
TrEMBLnew accessions      0 (0.0%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22537 (99.2%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   6137


GeneModel correction progress WS144 -> WS145
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    138  |    17  |
St Louis 	|     23  |     5  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|    597  |   -10  |
St Louis 	|    830  |    -8  |
		+---------+--------+



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

No synchronisation issues


For more info mail [email protected]

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

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

Experimental range data for RNAi experiments.

Connections between Genes and Aceview identifiers, Refseq identifiers

Update to latest Human IPI protein set.


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


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

One CDS does not have a GeneID


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


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

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

Model Changes
-------------

1/ New tag in the #Evidence hash

2/ Method to track experimental range data in microarray experiments
   
3/ Structure_data class to store high-throughput 3D-structure data 

For more details of the changes see the CVS repository:
    
     http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/wormbase/wspec/


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


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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