WS185

New release of WormBase WS185, Wormpep185 and Wormrna185 Fri Nov 30 17:11:38 GMT 2007


WS185 was built by the skin of my teeth
======================================================================

This directory includes:
i)   database.WS185.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS185           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS185-WS184.dbcomp         -   log file reporting difference from last release
v)   wormpep185.tar.gz          -   full Wormpep distribution corresponding to WS185
vi)   wormrna185.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS185.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS185.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS185.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS185.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS185.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.WS185.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS185.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS185.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:
----------------------------

       	WS185       	WS184      	change
----------------------------------------------
a    	32365949	32365949	  +0
c    	17779887	17779887	  +0
g    	17756036	17756036	  +0
t    	32365750	32365750	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100267622	100267622	  +0


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


Gene data set (Live C.elegans genes 29572)
------------------------------------------
Molecular_info              27868 (94.2%)
Concise_description         4859 (16.4%)
Reference                   7505 (25.4%)
WormBase_approved Gene name 15119 (51.1%)
RNAi_result                 20719 (70.1%)
Microarray_results          19948 (67.5%)
SAGE_transcript             18707 (63.3%)




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

There are 20168 CDS in autoace, 23624 when counting 3456 alternate splice forms.

The 23624 sequences contain  base pairs in total.

Modified entries      70
Deleted entries       29
New entries           55
Reappeared entries    1

Net change  +27



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8276 (35.0%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10959 (46.4%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4389 (18.6%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3627 (15.4%)
UniProtKB/TrEMBL accessions     19656 (83.2%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23283 (98.6%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name 13465


GeneModel correction progress WS184 -> WS185
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     59  |    -3  |
St Louis 	|    445  |   -45  |
		+---------+--------+


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 worm@sanger.ac.uk
-===================================================================================-



New Data:
---------
The C. remanei genome is fully integrated.  There are 26464 protein coding genes with 3798 of them having 
CGC names infered from C.elegans orthology.
Alignments of all nematode transcript data and the usual protein sets are also included. 

Brugia malayi is also updated as a "genome browser" only species in this release.

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


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


Known Problems:
---------------
C.remanei blastx self-hits have not been removed.

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

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


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


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


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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