WS204

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Release Notes

New release of WormBase WS204, Wormpep204 and Wormrna204 Fri Jun 26 20:17:06 BST 2009


WS204 was built by Anthony
======================================================================

This directory includes:
i)   database.WS204.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS204           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS204-WS203.dbcomp         -   log file reporting difference from last release
v)   wormpep204.tar.gz          -   full Wormpep distribution corresponding to WS204
vi)   wormrna204.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS204.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS204.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS204.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS204.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS204.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.WS204.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS204.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS204.gz   - Mappings between PCR products and overlapping Genes


Release notes on the web:
-------------------------
http://www.wormbase.org/wiki/index.php/Release_Schedule



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

       	WS204       	WS203      	change
----------------------------------------------
a    	32367418	32367418	  +0
c    	17780763	17780763	  +0
g    	17756943	17756943	  +0
t    	32367086	32367086	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100272210	100272210	  +0


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


Gene data set (Live C.elegans genes 39921)
------------------------------------------
Molecular_info              38212 (95.7%)
Concise_description         5593 (14%)
Reference                   13459 (33.7%)
WormBase_approved Gene name 25804 (64.6%)
RNAi_result                 22793 (57.1%)
Microarray_results          21046 (52.7%)
SAGE_transcript             19008 (47.6%)




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

There are 20184 CDS in autoace, 24052 when counting 3868 alternate splice forms.

The 24052 sequences contain 10,630,049 base pairs in total.

Modified entries      49
Deleted entries       13
New entries           33
Reappeared entries    2

Net change  +22

Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              9759 (40.6%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11506 (47.8%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2787 (11.6%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  23915 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23915 (99.4%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24143


GeneModel correction progress WS203 -> WS204
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|      0  |     0  |
St Louis 	|      0  |     0  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|      0  |     0  |
St Louis 	|      0  |     0  |
		+---------+--------+



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:
---------
This release includes the first inclusion in WormBase of the M. hapla genome.

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


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


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


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

Proposed Changes / Forthcoming Data:
-------------------------------------
The M.incognita genome will be included soon - maybe as a post release addition to 
this one!

Model Changes:
------------------------------------
Fixed Transposon white space issues.


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


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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