WS202

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Release letter

New release of WormBase WS202, Wormpep202 and Wormrna202 Tue Apr 28 16:02:08 BST 2009


WS202 was built by P. Davis (BUILDER SI0002 mk.6)
======================================================================

This directory includes:
i)   database.WS202.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS202           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS202-WS201.dbcomp         -   log file reporting difference from last release
v)   wormpep202.tar.gz          -   full Wormpep distribution corresponding to WS202
vi)   wormrna202.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS202.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS202.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS202.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS202.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS202.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.WS202.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS202.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS202.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:
----------------------------

       	WS202       	WS201      	change
----------------------------------------------
a    	32367418	32367418	  +0
c    	17780763	17780761	  +2
g    	17756943	17756943	  +0
t    	32367086	32367086	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100272210	100272208	  +2
Total number of bases has increased - please investigate ! 


Chromosomal Changes:
--------------------

Chromosome: III
6362931 6362930 0   ->   6362931 6362931 1
6363164 6363163 0   ->   6363165 6363165 1


Gene data set (Live C.elegans genes 39894)
------------------------------------------
Molecular_info              38185 (95.7%)
Concise_description         5547 (13.9%)
Reference                   13429 (33.7%)
WormBase_approved Gene name 25767 (64.6%)
RNAi_result                 22793 (57.1%)
Microarray_results          21050 (52.8%)
SAGE_transcript             18877 (47.3%)




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

There are 20181 CDS in autoace, 24029 when counting 3847 alternate splice forms.

The 24029 sequences contain 10,622,961 base pairs in total.

Modified entries      69
Deleted entries       38
New entries           73
Reappeared entries    2

Net change  +37
The differnce between the total CDS's of this (24029) and the last build (23993) does not equal the net change 37
Please investigate! ! 




Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8730 (36.3%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11743 (48.9%)	Some, but not all exon bases are covered by transcript evidence
Predicted              3556 (14.8%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  23801 (99.1%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23801 (99.1%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24107


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:
---------

1) tRNAs for C. briggsae and C. brenneri

2) TC1 Transposon annotation Update
WBTransposon objects replaceing old sequence based naming.

3) MIRAGE1 Transposon annotation Update

4) The Phenotype Ontology has been modified to curate nematode species other than the C. elegans \u201cN2\u201d strain. This includes a change in term names from \u201c_abnormal\u201d to \u201c_variant\u201d.  The old term names that included \u201cabnormal\u201d have been kept as synonyms so people used to these terms will still be able to find them. The ID's have NOT changed.

Example:

WBPhenotype:0000037:* egg_morphology_abnormal*
Def: "Any deviation in the overall structure or appearance of fertilized oocytes that are deposited by adult hermaphrodites.

*Changed to:*

WBPhenotype:0000037:* egg_morphology_variant*
Def: "Any variation in the overall structure or appearance of fertilized oocytes that are laid compared to those laid by control animals.
synonym: "egg_morphology_abnormal 



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

Two "C's" were added to C56G2 at bases 40730 and 40963.

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


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


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

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

1) C. elegans 454 sequence data for WASHU 
See the RNAseq_Mitreva_454_elegans Analysis object in WS203


Model Changes:
------------------------------------
None same as WS201


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


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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