WS188

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Release Notes

New release of WormBase WS188, Wormpep188 and Wormrna188 Fri Feb 29 14:53:33 GMT 2008


WS188 was built by [Michael Han (michael.paulini@wormbase.org)]
======================================================================

This directory includes:
i)   database.WS188.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS188           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS188-WS187.dbcomp         -   log file reporting difference from last release
v)   wormpep188.tar.gz          -   full Wormpep distribution corresponding to WS188
vi)   wormrna188.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS188.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS188.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS188.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS188.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS188.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.WS188.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS188.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS188.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:
----------------------------

       	WS188       	WS187      	change
----------------------------------------------
a    	32365950	32365950	  +0
c    	17779886	17779886	  +0
g    	17756037	17756037	  +0
t    	32365750	32365750	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100267623	100267623	  +0


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


Gene data set (Live C.elegans genes 29684)
------------------------------------------
Molecular_info              27983 (94.3%)
Concise_description         5203 (17.5%)
Reference                   7620 (25.7%)
WormBase_approved Gene name 15215 (51.3%)
RNAi_result                 20749 (69.9%)
Microarray_results          19972 (67.3%)
SAGE_transcript             18766 (63.2%)




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

There are 20178 CDS in autoace, 23693 when counting 3515 alternate splice forms.

The 23693 sequences contain  base pairs in total.

Modified entries      132
Deleted entries       27
New entries           55
Reappeared entries    3

Net change  +31



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8370 (35.3%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10956 (46.2%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4367 (18.4%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3676 (15.5%)
UniProtKB/TrEMBL accessions     19679 (83.1%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23355 (98.6%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  13564


GeneModel correction progress WS187 -> WS188
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|      0  |  -127  |
St Louis 	|      0  |  -404  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

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



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

No synchronisation issues


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



New Data:
---------
* updated C.briggsae genes / transcripts and BLAT alignments
* included new ESTs from WashU
 * ~2500 new C.brenneri ESTs
 * ~1600 new C.japonica ESTs
* added OMIM tags to ortholog H.sapiens genes
* added Inparanoid 6 data for C.elegans <-> H.sapiens orthologs

Genome sequence updates:
-----------------------
none

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


Known Problems:
---------------
Affymetrix / Agilent / GSC probe flatfiles will be made available at a later date.

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

Proposed Changes / Forthcoming Data:
-------------------------------------
changes to the CGH array alleles, to store gap between internal and external deletion points


Model Changes:
------------------------------------
new Evidence type Variation_evidence


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


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.

Fixes/Patches

microarray_probe tables

the missing files were released on 3rd of March 2008 at:

Inparanoid 6 human orthologs

For some Inparonoid 6 worm genes with human orthologs, a C.elegans gene is erroneously named as human ortholog.