WS191

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Release Notes

New release of WormBase WS191, Wormpep191 and Wormrna191 Mon Jun  2 09:50:52 BST 2008

WS191 was built by Mary Ann Tuli
======================================================================

This directory includes:
i)   database.WS191.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS191           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS191-WS190.dbcomp         -   log file reporting difference from last release
v)   wormpep191.tar.gz          -   full Wormpep distribution corresponding to WS191
vi)   wormrna191.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS191.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS191.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS191.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS191.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS191.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.WS191.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS191.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS191.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:
----------------------------

       	WS191       	WS190      	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 29821)
------------------------------------------
Molecular_info              28126 (94.3%)
Concise_description         5374 (18%)
Reference                   7725 (25.9%)
WormBase_approved Gene name 15353 (51.5%)
RNAi_result                 20808 (69.8%)
Microarray_results          20461 (68.6%)
SAGE_transcript             18840 (63.2%)




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

There are 20195 CDS in autoace, 23784 when counting 3589 alternate splice forms.

The 23784 sequences contain 10,458,215 base pairs in total.

Modified entries      27
Deleted entries       19
New entries           31
Reappeared entries    0

Net change  +12

Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8431 (35.4%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10965 (46.1%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4388 (18.4%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  23640 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23644 (99.4%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  13707


GeneModel correction progress WS190 -> WS191
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     42  |   -15  |
St Louis 	|    174  |     9  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

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



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

CHROMOSOME_II	sequence U40030

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



New Data:
---------
Blast database versions:
- yeast29.pep

Proposed Changes / Forthcoming Data:
-------------------------------------
nGASP gene predictions are beginning to be displayed through WormBase.  Genome browser views are already 
available for final elegans and briggsae predictions and component gene predictions for brenneri, japonica 
remanei and B. malayi.  These will be updated once final predictions are available.  Full integration, 
including orthologue determination and naming along with the presentation of gene pages etc will will occur 
over the forthcoming releases.

Model Changes:
------------------------------------
Added tags to connect CGH deletions that may hit genes.
?Variation.Possibly_affects ?Gene XREF Possibly_affected_by #Evidence
?Gene.Possibly_affected_by ?Variation XREF Possibly_affects #Evidence

Added score type tags to Interaction_info
#Interaction_info
 Confidence    Confidence_level        UNIQUE Float
 P_value

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


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.

____________  END _____________


Patches

  • Missing TreeFam ids