WS183

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Release Notes

New release of WormBase WS183, Wormpep183 and Wormrna183 Tue Oct 16 16:18:34 BST 2007


WS183 was built by Mary Ann Tuli
======================================================================

This directory includes:
i)   database.WS183.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS183           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS183-WS182.dbcomp         -   log file reporting difference from last release
v)   wormpep183.tar.gz          -   full Wormpep distribution corresponding to WS183
vi)   wormrna183.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS183.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS183.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS183.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS183.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS183.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.WS183.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS183.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS183.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:
----------------------------

       	WS183       	WS182      	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 29520)
------------------------------------------
Molecular_info              27811 (94.2%)
Concise_description         4942 (16.7%)
Reference                   7350 (24.9%)
WormBase_approved Gene name 14801 (50.1%)
RNAi_result                 20694 (70.1%)
Microarray_results          19937 (67.5%)
SAGE_transcript             18668 (63.2%)




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

There are 20155 CDS in autoace, 23541 when counting 3386 alternate splice forms.

The 23541 sequences contain  base pairs in total.

Modified entries      37
Deleted entries       81
New entries           25
Reappeared entries    0

Net change  -56
The differnce between the total CDS's of this (23541) and the last build (23523) does not equal the net change -56
Please investigate! ! 




Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8153 (34.6%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10990 (46.7%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4398 (18.7%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3608 (15.3%)
UniProtKB/TrEMBL accessions     19671 (83.6%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23279 (98.9%)



Gene <-> CDS,Transcript,Pseudogene connections (WormBase-approved)
---------------------------------------------
Entries with WormBase-approved Gene name  17151


GeneModel correction progress WS182 -> WS183
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    241  |    72  |
St Louis 	|    832  |   143  |
		+---------+--------+


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:
---------
1) 50,906 new SNPs submitted to St. Louis

2) The first copy number variant (CNV) data generated by array Comparative Genomic Hybridization (CGH) 
has been submitted to WormBase from The University of British Columbia, Vancouver Gene Knockout Laboratory.

3) We have assigned nearly 4000 approved gene names to non C.elegans genes (mainly C.briggsae).

4) We have updated the other-nematode ESTs used for BLATing using data from EMBL Release 91 (31-May-2007).

5) We have updated the RefSeq mapping.

6) We have added RST (RACE Sequence Tags) to the Splice_confirmation hash.

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


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


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


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

Proposed Changes / Forthcoming Data:
-------------------------------------
Forthcoming model changes
*************************
1) Removed UNIQUE from these lines
?Feature
History Acquires_merge UNIQUE ?Feature XREF Merged_into #Evidence

2) ?Operon
History Acquires_merge UNIQUE ?Operon XREF Merged_into #Evidence
Split_into UNIQUE ?Operon XREF Split_from #Evidence

3) Two new #Molecular_change subtags:
a) Regulatory_feature #Evidence // for cases where it overlaps a known feature
b) Genomic_neigborhood Text #Evidence // where it is in the "region" of a gene and might influence it

Model Changes:
------------------------------------
1) added RST to Splice_confirmation hash

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


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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