WS192

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New release of WormBase WS192, Wormpep192 and Wormrna192 Tue Jun 24 11:23:32 BST 2008


WS192 was built by Gary Williams
======================================================================

This directory includes:
i)   database.WS192.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS192           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS192-WS191.dbcomp         -   log file reporting difference from last release
v)   wormpep192.tar.gz          -   full Wormpep distribution corresponding to WS192
vi)   wormrna192.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS192.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS192.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS192.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS192.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS192.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.WS192.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS192.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS192.gz   - Mappings between PCR products and overlapping Genes


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



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

       	WS192       	WS191      	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 29849)
------------------------------------------
Molecular_info              28134 (94.3%)
Concise_description         5386 (18%)
Reference                   7783 (26.1%)
WormBase_approved Gene name 15410 (51.6%)
RNAi_result                 20812 (69.7%)
Microarray_results          20456 (68.5%)
SAGE_transcript             18838 (63.1%)




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

There are 20193 CDS in autoace, 23814 when counting 3621 alternate splice forms.

The 23814 sequences contain 10,473,024 base pairs in total.

Modified entries      66
Deleted entries       26
New entries           56
Reappeared entries    0

Net change  +30



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8451 (35.5%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10973 (46.1%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4390 (18.4%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  23675 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23675 (99.4%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  13744


GeneModel correction progress WS191 -> WS192
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     32  |   -10  |
St Louis 	|    152  |   -22  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

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



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

No synchronisation issues


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



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


Over 8000 new Mos transposon insertion alleles from the NemaGENETAG project have been added. 

Updates were made to the following database used for BLAST searches:

Flybase
IPI_human
Yeast

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

None.

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

None.

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

None.

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

None.

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

The website at [ftp://ftp.sanger.ac.uk/pub2/wormbase/WS192/genomes/ ftp://ftp.sanger.ac.uk/pub2/wormbase/WS192/genomes/] has
been reorganised to contain information from several nematode
species. These will be populated with data in the future as more
information becomes available.

corrected typo in the ?Antibody Model

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

Slight restructure of ?Antibody class

Well defined antibodies will be full populated with Isolation data.  Ambigous anibodies
will be connected to what it is believed to be by the Possible_pseudonym(_of) pair of tags
No connection to CDS is required - just Gene is fine


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


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 [http://www.acedb.org/ 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.