WS193

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release notes

New release of WormBase WS193, Wormpep193 and Wormrna193 Fri Jul 25 22:12:15 BST 2008


WS193 was built by Michael Han (mh6@sanger.ac.uk)
======================================================================

This directory includes:
i)   database.WS193.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS193           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS193-WS192.dbcomp         -   log file reporting difference from last release
v)   wormpep193.tar.gz          -   full Wormpep distribution corresponding to WS193
vi)   wormrna193.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS193.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS193.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS193.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS193.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS193.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.WS193.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS193.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS193.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:
----------------------------

       	WS193       	WS192      	change
----------------------------------------------
a    	32365950	32365950	  +0
c    	17779890	17779890	  +0
g    	17756040	17756040	  +0
t    	32365752	32365752	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100267632	100267632	  +0


Chromosomal Changes:
--------------------
There are no changes to the chromosome sequences in this release.


Gene data set (Live C.elegans genes 29874)
------------------------------------------
Molecular_info              28153 (94.2%)
Concise_description         5410 (18.1%)
Reference                   13167 (44.1%)
WormBase_approved Gene name 15503 (51.9%)
RNAi_result                 20817 (69.7%)
Microarray_results          20460 (68.5%)
SAGE_transcript             18848 (63.1%)




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

There are 20195 CDS in autoace, 23864 when counting 3621 alternate splice forms.

The 23864 sequences contain 10,473,024 base pairs in total.

Modified entries      74
Deleted entries       40
New entries           86
Reappeared entries    0

Net change  +50




Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8483 (35.5%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10985 (46.0%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4396 (18.4%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  23727 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23731 (99.4%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  13831


GeneModel correction progress WS192 -> WS193
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     30  |    -2  |
St Louis 	|    145  |    -7  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|      6  |     0  |
St Louis 	|      6  |     0  |
		+---------+--------+



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

CHROMOSOME_I	sequence AC024201
CHROMOSOME_III	sequence AC087081
CHROMOSOME_III	sequence U13019
CHROMOSOME_III	sequence AC006605
CHROMOSOME_IV	sequence AF067612
CHROMOSOME_IV	sequence AC025715
CHROMOSOME_IV	sequence AC025724
CHROMOSOME_X	sequence U41550
CHROMOSOME_X	sequence AC084152

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



New Data:
---------
The newly released Treefam-6 data was imported.
The Flybase blast database was updated.
WormBase-Compara orthology prediction is now using a tree-based method to be more in line with
TreeFam and EnsEMBL-Compara.

The WormBase C.remanei data was updated using a set of Jigsaw gene-models provided by NGASP 
on the new WashU C.remanei cr15 assembly.
Old gene-ids were mapped onto the new models where possible, to enable tracking and  new
C.remanei genes annotated with CGC/WGN-Names based on ortholog C.elegans genes.
Starting with WS194 manual curation of C.remanei gene models will begin.

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


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


Known Problems:
---------------
The Anomalies-GFF files will be provided later as separate downloads.

Other Changes:
--------------
Phenotype naming changed to WBPhenotype:XYZ

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

For WS194 an improved set of C.briggsae genes will be provided from a combination of NGASP predictions
and manually curation.

Pristionchus pacificus data will be made available at WormBase through a cooperation with the Sommer Lab at the
MPG Tuebingen.

Basepair Conservation Scores from PECAN+GERP will be made available as GBrowse wiggle tracks.

OMIM data and Mammalian orthologs will be imported from the EnsEMBL-50/WS190 release and attached to proteins.

3 genomic changes will be made on the C.elegans reference sequence:
F36H1   1bp insertion       
B0024   1bp deletion    
C18E9   1bp deletion 

Model Changes:
------------------------------------
corrected a typo in ?Antibody

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


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.

____________  END _____________

patches

curation anomalies GFFs

  • C.elegans can be found here
  • C.remanei can be found here

missing protein data

  • The C.remanei protein patch can be found here