WS189

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Release Notes

New release of WormBase WS189, Wormpep189 and Wormrna189 Thu Apr  3 10:28:39 BST 2008


WS189 was built by [Paul Davis (paul.davis@wormbase.org)]
======================================================================

This directory includes:
i)   database.WS189.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS189           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS189-WS188.dbcomp         -   log file reporting difference from last release
v)   wormpep189.tar.gz          -   full Wormpep distribution corresponding to WS189
vi)   wormrna189.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS189.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS189.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS189.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS189.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS189.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.WS189.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS189.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS189.gz   - Mappings between PCR products and overlapping Genes


Release notes on the web:
-------------------------
http://www.wormbase.org/wiki/index.php/Release_notes



Genome sequence composition:
----------------------------

       	WS189       	WS188      	change
----------------------------------------------
a    	32365950	32365950	  +0
c    	17779890	17779886	  +4
g    	17756040	17756037	  +3
t    	32365752	32365750	  +2
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100267632	100267623	  +9
Total number of bases has increased - please investigate ! 


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

Chromosome: II
5216407 5216406 0   ->   5216393 5216393 1
5237996 5237995 0   ->   5237983 5237983 1
6740248 6740247 0   ->   6740236 6740236 1
6768189 6768188 0   ->   6768178 6768178 1
6769614 6769613 0   ->   6769604 6769604 1
6769866 6769865 0   ->   6769857 6769857 1
7040881 7040880 0   ->   7040873 7040873 1

Chromosome: X
385737 385736 0   ->   385724 385724 1
3915184 3915183 0   ->   3915172 3915172 1


Gene data set (Live C.elegans genes 29790)
------------------------------------------
Molecular_info              28092 (94.3%)
Concise_description         5268 (17.7%)
Reference                   7676 (25.8%)
WormBase_approved Gene name 15253 (51.2%)
RNAi_result                 20787 (69.8%)
Microarray_results          19995 (67.1%)
SAGE_transcript             18825 (63.2%)




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

There are 20181 CDS in autoace, 23727 when counting 3546 alternate splice forms.

The 23727 sequences contain 10427754 base pairs in total.

Modified entries      201
Deleted entries       43
New entries           76
Reappeared entries    0

Net change  +33




Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8390 (35.4%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10955 (46.2%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4382 (18.5%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  23581 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23581 (99.4%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  13605


GeneModel correction progress WS188 -> WS189
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     66  |   -61  |
St Louis 	|    119  |  -149  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|      5  |    -1  |
St Louis 	|      5  |    -1  |
		+---------+--------+



Synchronisation with GenBank / EMBL:
------------------------------------

CHROMOSOME_II	sequence U46753
CHROMOSOME_II	sequence U39471
CHROMOSOME_II	sequence U39999
CHROMOSOME_II	sequence U40030
CHROMOSOME_II	sequence U58758
CHROMOSOME_X	sequence U41550
CHROMOSOME_X	sequence AF047662

There are no gaps remaining in the genome sequence
---------------
For more info mail help@wormbase.org
-===================================================================================-



New Data:
---------


Genome sequence updates:
-----------------------
9 bp were added to WS189

R04A9  added 1 C at 14053
T16D1  added 1 C at 2003
C34F11 added 1 C at 31960
ZK1127 added 1 G at 6864
T22B2  added 1 T at 14160
T14B4  added 1 C at 35584
F41G3  added 1 G at 28352
 "     added 1 T at 29776
 "     added 1 C at 30031



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


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


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


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


Model Changes:
------------------------------------
added tags to store gap between internal and external deletion points for CGH alleles.

known problems

CGH probe mapping

Some CGH probes got wrong negative coordinates in the GFF files.

WormBase-compara

The WormBase compara data was missing from WS189. A patchfile based on WS190 was made and is available at ftp://ftp.sanger.ac.uk/pub2/wormbase/WS189/compara_patch.ace