WS210

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New release of WormBase WS210, Wormpep210 and Wormrna210 Tue Dec 22 12:35:31 GMT 2009


WS210 was built by Gary Williams
======================================================================

This directory includes:
i)   database.WS210.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS210           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS210-WS209.dbcomp         -   log file reporting difference from last release
v)   wormpep210.tar.gz          -   full Wormpep distribution corresponding to WS210
vi)   wormrna210.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS210.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS210.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS210.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS210.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS210.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.WS210.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS210.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS210.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:
----------------------------

       	WS210       	WS209      	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 40052)
------------------------------------------
Molecular_info              38350 (95.8%)
Concise_description         5615 (14%)
Reference                   13714 (34.2%)
WormBase_approved Gene name 25858 (64.6%)
RNAi_result                 24280 (60.6%)
Microarray_results          21063 (52.6%)
SAGE_transcript             19069 (47.6%)




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

There are 20254 CDS in autoace, 24273 when counting 4019 alternate splice forms.

The 24273 sequences contain 10,732,870 base pairs in total.

Modified entries      48
Deleted entries       28
New entries           65
Reappeared entries    2

Net change  +39




Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              9922 (40.9%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11599 (47.8%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2752 (11.3%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  24137 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            24137 (99.4%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24204


GeneModel correction progress WS209 -> WS210
-----------------------------------------
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:
---------

Blast databases updated:
brigpep210
ipi_human_11_06
gadfly36
remapep210
wormpep210
yeast38


This release includes 151 Feature objects marking the positions of
probable genome sequence errors.

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://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

It is expected that these probable genome sequence error positions wil be examined and corrected soon.

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


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


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


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

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

added Feature to Feature connection

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

added Assistant professor to #Role

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


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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