WS206

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Release Notes

New release of WormBase WS206, Wormpep206 and Wormrna206 Fri Aug 28 13:06:57 BST 2009


WS206 was built by Gary Williams (gw3@sanger.ac.uk)
======================================================================

This directory includes:
i)   database.WS206.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS206           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS206-WS205.dbcomp         -   log file reporting difference from last release
v)   wormpep206.tar.gz          -   full Wormpep distribution corresponding to WS206
vi)   wormrna206.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS206.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS206.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS206.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS206.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS206.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.WS206.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS206.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS206.gz   - Mappings between PCR products and overlapping Genes


Release notes on the web:
-------------------------
http://www.wormbase.org/wiki/index.php/Release_Schedule



Genome sequence composition:
----------------------------

       	WS206       	WS205      	change
----------------------------------------------
a    	32367418	32367418	  +0
c    	17780763	17780763	  +0
g    	17756943	17756943	  +0
t    	32367086	32367086	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100272210	100272210	  +0


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


Gene data set (Live C.elegans genes 39962)
------------------------------------------
Molecular_info              38256 (95.7%)
Concise_description         5597 (14%)
Reference                   13639 (34.1%)
WormBase_approved Gene name 25832 (64.6%)
RNAi_result                 22816 (57.1%)
Microarray_results          21050 (52.7%)
SAGE_transcript             19037 (47.6%)




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

There are 20209 CDS in autoace, 24143 when counting 3934 alternate splice forms.

The 24143 sequences contain 10,671,996 base pairs in total.

Modified entries      69
Deleted entries       17
New entries           46
Reappeared entries    1

Net change  +30
The differnce between the total CDS's of this (24143) and the last build (24114) does not equal the net change 30
Please investigate! ! 




Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              9811 (40.6%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11543 (47.8%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2789 (11.6%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  23999 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23999 (99.4%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24174


GeneModel correction progress WS205 -> WS206
-----------------------------------------
Confirmed introns not in a CDS gene model;

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


Members of known repeat families that overlap predicted exons;

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



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:
---------


WS206 includes data from Marcel Tijsterman et al. "Isolation of
deletion alleles by G4 DNA-induced mutagenesis" Nature Mathods (in
press)

 the abstract is :
"Metazoan genomes contain thousands of sequence tracts that match the
G4 DNA signature G3NxG3NxG3NxG3, a motif that is intrinsically
mutagenic, probably because it can form secondary structures during
DNA replication.  Here we show how, and to what extent, this feature
can be used to generate deletion alleles of many C. elegans genes."

The OMA orthology predictions from the OMA Orthologs Matrix Project
http://www.cbrg.ethz.ch/research/orthologous have been updated to the
June 2009 release.

Inparanoid has been updated to release 7

The cisRed (conserved genomic elements) supplementary GFF files (with
an p-value cutoff 0.05) has been added.  Downloaded from the cisRED
database: http://www.cisred.org/

The BLAST database for IPI, yeast, and flybase were updated.

InterPro data was updated to release 22


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


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


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


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

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

added DB_info to Anatomy_term


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

Fixed Transposon white space issues.



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


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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