WS205

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Release Letter

New release of WormBase WS205, Wormpep205 and Wormrna205 Wed Jul 22 10:29:27 BST 2009


WS205 was built by Michael Han (<mh6@sanger.ac.uk>)
======================================================================

This directory includes:
i)   database.WS205.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS205           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS205-WS204.dbcomp         -   log file reporting difference from last release
v)   wormpep205.tar.gz          -   full Wormpep distribution corresponding to WS205
vi)   wormrna205.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS205.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS205.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS205.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS205.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS205.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.WS205.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS205.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS205.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:
----------------------------

       	WS205       	WS204      	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 39951)
------------------------------------------
Molecular_info              38244 (95.7%)
Concise_description         5592 (14%)
Reference                   13539 (33.9%)
WormBase_approved Gene name 25815 (64.6%)
RNAi_result                 22803 (57.1%)
Microarray_results          21047 (52.7%)
SAGE_transcript             19028 (47.6%)




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

There are 20197 CDS in autoace, 24114 when counting 3917 alternate splice forms.

The 24114 sequences contain 10,659,313 base pairs in total.

Modified entries      59
Deleted entries       44
New entries           106
Reappeared entries    0

Net change  +62



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              9790 (40.6%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11535 (47.8%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2789 (11.6%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  23966 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23966 (99.4%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24156


GeneModel correction progress WS204 -> WS205
-----------------------------------------
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:
---------
* new and updated data from the C.elegans Gene Knockout Consortium
* new and updated knockout data from the National BioResource Project (NBRP)
* Meloidogyne incognita genome added to WormBase as Tier III species
* Paralog predictions added to Tier I/II species genes from wormbase-compara
* updated C.elegans and C.brenneri databases

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


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


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


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

Proposed Changes / Forthcoming Data:
-------------------------------------
* Operon updates for chromosome I/II/X based on modEncode/Waterstone short read data
* Orthology Matrix (OMA) updates from ETH Zurich
* repeat library updates for Tier II species from Ismael Vergara (Jack Chen lab)
* potential Caenorhabditis japonica genome assembly changes (WashU)
* Heterorhabditis bacteriophora genome

Model Changes:
------------------------------------


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


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 20-30 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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