WS198

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Release Letter

New release of WormBase WS198, Wormpep198 and Wormrna198 Thu Dec 18 19:31:36 GMT 2008


WS198 was built by [Michael Han (mh6@sanger.ac.uk)]
======================================================================

This directory includes:
i)   database.WS198.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS198           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS198-WS197.dbcomp         -   log file reporting difference from last release
v)   wormpep198.tar.gz          -   full Wormpep distribution corresponding to WS198
vi)   wormrna198.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS198.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS198.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS198.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS198.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS198.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.WS198.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS198.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS198.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:
----------------------------

       	WS198       	WS197      	change
----------------------------------------------
a    	32367419	32367419	  +0
c    	17780761	17780761	  +0
g    	17756942	17756942	  +0
t    	32367086	32367086	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100272208	100272208	  +0


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


Gene data set (Live C.elegans genes 39877)
------------------------------------------
Molecular_info              35565 (89.2%)
Concise_description         5523 (13.9%)
Reference                   13308 (33.4%)
WormBase_approved Gene name 25699 (64.4%)
RNAi_result                 22056 (55.3%)
Microarray_results          20723 (52%)
SAGE_transcript             18847 (47.3%)




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

There are 20186 CDS in autoace, 23962 when counting 3776 alternate splice forms.

The 23962 sequences contain 10,565,187 base pairs in total.

Modified entries      44
Deleted entries       27
New entries           50
Reappeared entries    480

Net change  +503



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8688 (36.3%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11719 (48.9%)	Some, but not all exon bases are covered by transcript evidence
Predicted              3555 (14.8%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  21826 (91.1%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            21826 (91.1%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  21436


GeneModel correction progress WS197 -> WS198
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|      0  |   -38  |
St Louis 	|      0  |  -118  |
		+---------+--------+


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 help@wormbase.org
-===================================================================================-


C.elegans , C.brenneri and C.remanei were updated for WS198.

New Data:
---------
A large curation effort was done on the C.brenneri gene predictions, reducing the
number of potentially erroneous gene models by half.


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


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


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


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

Proposed Changes / Forthcoming Data:
-------------------------------------
Some model changes in preparation for short-read expression data.

Model Changes:
------------------------------------
Added a Allow_misalign tag to the Homol_data class to allow exact AND fuzzy matches.


-===================================================================================-
Merry Christmas / Hanukkah / winter solstice / ... from Michael

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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