WS160

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New release of WormBase WS160, Wormpep160 and Wormrna160 Thu Jun 15 16:29:46 BST 2006


WS160 was built by Ant and Michael
======================================================================

This directory includes:
i)   database.WS160.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS160           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS160-WS159.dbcomp         -   log file reporting difference from last release
v)   wormpep160.tar.gz          -   full Wormpep distribution corresponding to WS160
vi)   wormrna160.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS160.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS160.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS160.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS160.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS160.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.WS160.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS160.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS160.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:
----------------------------

       	WS160       	WS159      	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 23757)
------------------------------------------
Molecular_info              22014 (92.7%)
Concise_description          4180 (17.6%)
Reference                    5879 (24.7%)
CGC_approved Gene name       8801 (37%)
RNAi_result                 19798 (83.3%)
Microarray_results          19126 (80.5%)
SAGE_transcript             18174 (76.5%)

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

There are 20063 CDS in autoace, 23144 when counting 3081 alternate splice forms.

The 23144 sequences contain 10,164,788 base pairs in total.

Modified entries              38
Deleted entries               47
New entries                   18
Reappeared entries             3

Net change  -26



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              6712 (29.0%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11424 (49.4%)	Some, but not all exon bases are covered by transcript evidence
Predicted              5008 (21.6%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3227 (13.9%)
UniProtKB/TrEMBL accessions     19623 (84.8%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22850 (98.7%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   7114


GeneModel correction progress WS159 -> WS160
-----------------------------------------
Confirmed introns not in a CDS gene model;

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


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|     63  |    -   |
St Louis 	|     121 |    -   |
		+---------+--------+



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

No synchronisation issues


There are no gaps remaining in the genome sequence
---------------
For more info mail help@wormbase.org
-===================================================================================-



New Data:
---------
There are ~18,000 new predicted interactions taken from "Zhong and Sternberg Science:Vol.311. pp.1481-1484"

~1300 new mos insertion alleles from the nemeGENTAG consortium

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


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


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

Proposed Changes / Forthcoming Data:
------------------------------------
New data models have been devised and agreed to allow the incorporation of Mass Spec protein analysis data to be included in WormBase.
We have data from several researchers, some of which will be inlcuded in a forthcoming release of the database.


Model Changes:
------------------------------------
Changes to Interaction and Interaction_type to allow inclusion of predicted interaction 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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