WS211

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Release Letter

New release of WormBase WS211, Wormpep211 and Wormrna211 Fri Jan 29 13:26:05 GMT 2010


WS211 was built by Paul Davis
======================================================================

This directory includes:
i)   database.WS211.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS211           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS211-WS210.dbcomp         -   log file reporting difference from last release
v)   wormpep211.tar.gz          -   full Wormpep distribution corresponding to WS211
vi)   wormrna211.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS211.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS211.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS211.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS211.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS211.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.WS211.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS211.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS211.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:
----------------------------

       	WS211       	WS210      	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 40067)
------------------------------------------
Molecular_info              38367 (95.8%)
Concise_description         5614 (14%)
Reference                   13750 (34.3%)
WormBase_approved Gene name 25859 (64.5%)
RNAi_result                 24177 (60.3%)
Microarray_results          21064 (52.6%)
SAGE_transcript             19082 (47.6%)




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

There are 20269 CDS in autoace, 24305 when counting 4036 alternate splice forms.

The 24305 sequences contain 10,741,119 base pairs in total.

Modified entries      44
Deleted entries       13
New entries           45
Reappeared entries    1

Net change  +33


Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              9938 (40.9%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11613 (47.8%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2754 (11.3%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  24168 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            24168 (99.4%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24207



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:
---------
10,572 new Feature sites including SL1 and SL2 trans-spliced sequence sites, poly-A 
sites and putative translation start and translation end sites have been added to this release.

Contigs of short reads which confirm these Features or which confirm introns have also been 
added as Sequence objects.

This data is derived from analyses of the RNAseq data from LaDeana
Hillier and Bob Waterston:

Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. 
http://tinyurl.com/y9cg9p9
pubmedID:19181841
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:
--------------
The Non-elegans blastx data is no longer loaded into the full acedb database release.

If you require a complete database with all data for each species you will have to 
install acedb as usual from

ftp://ftp.sanger.ac.uk/pub/wormbase/WS211/acedb/

and then load in the blastx data under:

ftp://ftp.sanger.ac.uk/pub/wormbase/WS211/acedb/Non_C_elegans_BLASTX/

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


Model Changes:
------------------------------------
Added tags to allow 2 features to be associated with each other.

Example:

If there are a rair of identical features mapping to different loci

?Feature
Associations	Associated_with_Feature ?Feature XREF Associated_with_Feature #Evidence

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


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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