WS213

Release Letter

New release of WormBase WS213, Wormpep213 and Wormrna213 Tue Mar 23 16:36:18 GMT 2010


WS213 was built by [Michael Paulini <mh6@sanger.ac.uk>]
======================================================================

This directory includes:
i)   database.WS213.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS213           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS213-WS212.dbcomp         -   log file reporting difference from last release
v)   wormpep213.tar.gz          -   full Wormpep distribution corresponding to WS213
vi)   wormrna213.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS213.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS213.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS213.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS213.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS213.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.WS213.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS213.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS213.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:
----------------------------

       	WS213       	WS212      	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 40136)
------------------------------------------
Molecular_info              38439 (95.8%)
Concise_description         5642 (14.1%)
Reference                   13819 (34.4%)
WormBase_approved Gene name 25896 (64.5%)
RNAi_result                 24204 (60.3%)
Microarray_results          21065 (52.5%)
SAGE_transcript             19102 (47.6%)




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

There are 20316 CDS in autoace, 24511 when counting 4195 alternate splice forms.

The 24511 sequences contain 10,826,126 base pairs in total.

Modified entries      40
Deleted entries       64
New entries           213
Reappeared entries    2

Net change  +151




Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed             10071 (41.1%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11718 (47.8%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2722 (11.1%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  24337 (99.3%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            24337 (99.3%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24247


GeneModel correction progress WS212 -> WS213
-----------------------------------------
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:
---------
Jack Chen that his group have generated genome-wide predictions for protein-coding genes in briggsae, remanei, brenneri, and japonica. These are based on the homologous C. elegans genes.

This data is produced by the genBlastG program which is a development of the genBlastA program:

  http://dx.doi.org/10.1101/gr.082081.108

Nota Bene that these data are being provided in advance of publication of the five-genome paper (coordinated by Erich Schwartz).


ncRNA entries were extended to include primary as well as mature transcripts and updated using mirbase and RFAM.

Genome sequence updates:
-----------------------
none

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


Known Problems:
---------------
Some RNAi mappings are a bit erratic. A fix will be forthcoming.
Some Gene Ontology terms are outdated (update planned for WS214)

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

Proposed Changes / Forthcoming Data:
-------------------------------------
The Gene Ontology used by WormBase will be updated for WS214
The Journal class will be removed with WS214, as it's functionality is covered by other classes.


Model Changes:
------------------------------------
the planned removal of the Journal class is postponed until WS214

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


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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