WormBase release WS170 now online

This is an automatic announcement that WormBase
(http://www.wormbase.org) has just been updated.  New releases occur
roughly every three weeks.

The text of the AceDB release notes, which contains highlights of the
new data is attached.  You can download the full AceDB files from:

   ftp://ftp.sanger.ac.uk/pub/wormbase/current_release/
   or
   ftp://ftp.wormbase.org/pub/wormbase/acedb/current_release

Additional information on the release, including any necessary patches or bug
fixes can be found on the WormBaseWiki:

   http://www.wormbase.org/wiki/index.php/WSWS170

New release of WormBase WS170, Wormpep170 and Wormrna170 Fri Jan 19 09:31:14 GMT 2007


WS170 was built by Paul Davis
======================================================================

This directory includes:
i)   database.WS170.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS170           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS170-WS169.dbcomp         -   log file reporting difference from last release
v)   wormpep170.tar.gz          -   full Wormpep distribution corresponding to WS170
vi)   wormrna170.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS170.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS170.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS170.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS170.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS170.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.WS170.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS170.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS170.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:
----------------------------

       	WS170       	WS169      	change
----------------------------------------------
a    	32365889	32365889	  +0
c    	17779856	17779856	  +0
g    	17756016	17756016	  +0
t    	32365689	32365689	  +0
n    	0       	0       	  +0

Total	100267450	100267450	  +0


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


Gene data set (Live C.elegans genes 23977)
------------------------------------------
Molecular_info              22281 (92.9%)
Concise_description          4380 (18.3%)
Reference                    6708 (28%)
CGC_approved Gene name       8940 (37.3%)
RNAi_result                 19842 (82.8%)
Microarray_results          19134 (79.8%)
SAGE_transcript             20020 (83.5%)




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

There are 20082 CDS in autoace, 23224 when counting 3142 alternate splice forms.

The 23224 sequences contain 10,186,194 base pairs in total.

Modified entries              24
Deleted entries               13
New entries                   16
Reappeared entries             0

Net change  +3



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              7825 (33.7%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10746 (46.3%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4653 (20.0%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3269 (14.1%)
UniProtKB/TrEMBL accessions     19437 (83.7%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22706 (97.8%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   7298


GeneModel correction progress WS169 -> WS170
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     15  |     0  |
St Louis 	|     10  |    -1  |
		+---------+--------+


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 [email protected]
-===================================================================================-



New Data:
---------
1) If you are planning to run mass spectrometry experiments, you might like to search the 
   file of translated open reading frames in:
   ftp://ftp.sanger.ac.uk/pub/wormbase/data/translated_orfs.WS170.gz
   in addition to the set of curated wormpep proteins.

   If you have questions about submitting any types of data to wormbase, please contact: [email protected]"

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


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


Known Problems:
---------------
1) 16 elegans peptides failed to run through the blastp pipeline.

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

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


Model Changes:
------------------------------------
PaulD
Added tag to ?Operon to track removed operons and #Evidence to the Remark.

?Operon
History         Deprecated     Text     #Evidence
Remark        Text     #Evidence

further operon related addition.
?Trans_splice_leader . Inferred #Evidence


==========================================================================================================
MichealH
Removed the erroneous UNIQUE from the Ortholog_other tag added last time. It is actually not needed at all.

?Gene
Ortholog_other  ?Database ?Database_field ?Accession_number ?Species #Evidence

==========================================================================================================
GaryW
Corrected type in Protein class introduced last time

?Protein
    Contains_peptide ?Mass_spec_peptonide     <----


==========================================================================================================
Igor/Raymond
?Expression_cluster and ?Anatomy_term changes to describe microarray experiments involving expression profiling in a particular tissue or cell.

?Expression_cluster Anatomy_term ?Anatomy_term XREF Expression_cluster #Evidence

?Anatomy_term Attribute_of Expression_cluster ?Expression_cluster XREF Anatomy_term #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.

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