WS209

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Release Notes

New release of WormBase WS209, Wormpep209 and Wormrna209 Fri Nov 27 11:57:36 GMT 2009


WS209 was built by [Michael Han]
======================================================================

This directory includes:
i)   database.WS209.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS209           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS209-WS208.dbcomp         -   log file reporting difference from last release
v)   wormpep209.tar.gz          -   full Wormpep distribution corresponding to WS209
vi)   wormrna209.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS209.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS209.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS209.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS209.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS209.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.WS209.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS209.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS209.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:
----------------------------

       	WS209       	WS208      	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 40034)
------------------------------------------
Molecular_info              38329 (95.7%)
Concise_description         5612 (14%)
Reference                   13654 (34.1%)
WormBase_approved Gene name 25848 (64.6%)
RNAi_result                 24271 (60.6%)
Microarray_results          21060 (52.6%)
SAGE_transcript             19063 (47.6%)




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

There are 20245 CDS in autoace, 24236 when counting 3991 alternate splice forms.

The 24236 sequences contain 10,713,280 base pairs in total.

Modified entries      49
Deleted entries       28
New entries           62
Reappeared entries    0

Net change  +34



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              9868 (40.7%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11615 (47.9%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2753 (11.4%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  24100 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            24100 (99.4%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24191


GeneModel correction progress WS208 -> WS209
-----------------------------------------
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 coding transcripts predicted from the RNA-Seq project in 14 different life-stages and strains by LaDeana Hillier and Bob Waterston:

Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. <http://www.ncbi.nlm.nih.gov/pubmed/19181841?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=1>

Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH.

Genome Res. 2009 Apr;19(4):657-66. Epub 2009 Jan 30.PMID: 19181841


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


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


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


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


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


Model Changes:
------------------------------------
Added / modified tags to better classify pseudogenes.

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


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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