WS184

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ew release of WormBase WS184, Wormpep184 and Wormrna184 Thu Nov  8 12:09:34 GMT 2007


WS184 was built by Paul Davis
======================================================================

This directory includes:
i)   database.WS184.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS184           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS184-WS183.dbcomp         -   log file reporting difference from last release
v)   wormpep184.tar.gz          -   full Wormpep distribution corresponding to WS184
vi)   wormrna184.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS184.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS184.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS184.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS184.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS184.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.WS184.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS184.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS184.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:
----------------------------

       	WS184       	WS183      	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 29548)
------------------------------------------
Molecular_info              27841 (94.2%)
Concise_description         5003 (16.9%)
Reference                   7399 (25%)
WormBase_approved Gene name 15005 (50.8%)
RNAi_result                 20705 (70.1%)
Microarray_results          19948 (67.5%)
SAGE_transcript             18695 (63.3%)




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

There are 20168 CDS in autoace, 23597 when counting 3429 alternate splice forms.

The 23597 sequences contain  base pairs in total.

Modified entries      82
Deleted entries       37
New entries           91
Reappeared entries    2

Net change  +56



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8255 (35.0%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11066 (46.9%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4276 (18.1%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3615 (15.3%)
UniProtKB/TrEMBL accessions     19659 (83.3%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23274 (98.6%)



Gene <-> CDS,Transcript,Pseudogene connections (WormBase-approved)
---------------------------------------------
Entries with WormBase-approved Gene name  18119


GeneModel correction progress WS183 -> WS184
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     62  |  -179  |
St Louis 	|    490  |  -342  |
		+---------+--------+


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) ensembl orthologs updated to be from EnsEMBL  release 47 / WS180

2) nematode EST sequences of species not represented in WormBase were  updated for BLAT from EMBL release 91.

3) Ortholog predictions for C.elegans and C.briggsae were added to  WormBase based on The OMA Orthologs Matrix Project (C Dessimoz et al. 2005).

4) Existing ortholog predictions were updated for TreeFam 5 and  Inparanoid 6.

5) ~5000 C. briggsae genes assigned wormbase approved (GNW) names.

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


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


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


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

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

1) ~3 million new oligo_set objects from the Affymetrix tiling array.

2) C. remanei will be fully integrated into WS185 to the same level as C. brioggsae.
   This integration will include:
      Stable gene IDs for current gene set.
      Better Orthologue assignment.
      Gene pages.
      Protein pages.
      Blast hits.
      etc.

3) TreeFam 5 and Inparanoid 6 ortholog predictions for C.remanei will be  included in WS185.

4) PECAN data to be included for elegans/briggsae/remanei/(pre-release)brenneri
   clustalw files
   gff data in main gff files
   mysql database dumps

Model Changes:
------------------------------------
Removed UNIQUE from these lines
?Feature
History Acquires_merge UNIQUE ?Feature XREF Merged_into #Evidence

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

Added some new tags in  
#Molecular_change
Regulatory_feature #Evidence // for cases where it overlaps a known feature
Genomic_neigborhood Text #Evidence // where it is in the "region" of a gene and might influence it

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


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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