WormBase release WS176 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/WSWS176

new release of WormBase WS176, Wormpep176 and Wormrna176 Mon May 21 11:58:06 BST 2007


WS176 was built by Mry Ann Tuli
======================================================================

This directory includes:
i)   database.WS176.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS176           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS176-WS175.dbcomp         -   log file reporting difference from last release
v)   wormpep176.tar.gz          -   full Wormpep distribution corresponding to WS176
vi)   wormrna176.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS176.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS176.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS176.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS176.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS176.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.WS176.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS176.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS176.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:
----------------------------

       	WS176       	WS175      	change
----------------------------------------------
a    	32365889	32365889	  +0
c    	17779856	17779856	  +0
g    	17756016	17756016	  +0
t    	32365689	32365689	  +0
n    	0       	0       	  +0

Total	100267451	100267502	 -51
Total number of bases has decreased - please investigate ! 


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


Gene data set (Live C.elegans genes 24101)
------------------------------------------
Molecular_info              22410 (93%)
Concise_description          4578 (19%)
Reference                    7003 (29.1%)
CGC_approved Gene name       9213 (38.2%)
RNAi_result                 19876 (82.5%)
Microarray_results          19152 (79.5%)
SAGE_transcript             20034 (83.1%)

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

There are 20131 CDS in autoace, 23375 when counting 3244 alternate  splice forms.

The 23375 sequences contain 10,266,608 base pairs in total.

Modified entries              91
Deleted entries               77
New entries                  175
Reappeared entries             4

Net change  +102


Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              7940 (34.0%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10811 (46.3%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4624 (19.8%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3523 (15.1%)
UniProtKB/TrEMBL accessions     19412 (83.0%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22935 (98.1%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   7573


GeneModel correction progress WS175 -> WS176
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     70  |  -103  |
St Louis 	|    179  |   -33  |
		+---------+--------+


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:
---------
 A set of 51,623 mass spectroscopy peptides from Gennifer Merrihew at Michael MacCoss's laboratory 
has been added to this release.  Proteins have been fragmented and the molecular weights of the 
fragments have then been used to deduce the sequence of the fragments by comparing to a database 
of C. elegans protein sequences.

 The peptides were mapped to the genome using the known positions of the peptides in the matching 
proteins and the known positions of the proteins' genes on the genome.

 This data gives confirmatory evidence of many exons and (where they span splice sites) some introns.


Genome sequence updates:
-----------------------
None

New Fixes:
----------
None

Known Problems:
---------------
None

Other Changes:
--------------
None

Proposed Changes / Forthcoming Data:
-------------------------------------
A number of genomic canonical clones are going to be updated for WS177.

F54F7   deletion  tagctcaccagcttgcacgGgaagtgaaagtcttgaaata
F28H7   deletion  aacaaaatcttgcaactagTaatgtgaaaaagtgtggact
K07A1   insertion ttctcaaatttcagtttatTggaacattacaaatatgtgt
F13G3   insertion tttttttcagacaccgttcgtttggctccgGcgcgatcaacatggtgatggttgcacaagg
R10E11  deletion  gccacctggaaatcaatcagctcctcaaaaAgaattccgaatctgcctatattctgttcta
K11H3   insertion gcattaacaacacacggaaatcgaaatggaCcacttcgttatagtcttcttcaacaacgag
F13G3   insertion ccttgtgcaaccatcaccatgttgatcgcgGcggagccaaacgaacggtgtctgaaaaaaa
Y95D11A shift-overlap with F49D11


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


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


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.

____________  END _____________