WormBase release WS171 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/WSWS171

New release of WormBase WS171, Wormpep171 and Wormrna171 Thu Feb  8 15:28:27 GMT 2007


WS171 was built by Anthony
======================================================================

This directory includes:
i)   database.WS171.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS171           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS171-WS170.dbcomp         -   log file reporting difference from last release
v)   wormpep171.tar.gz          -   full Wormpep distribution corresponding to WS171
vi)   wormrna171.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS171.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS171.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS171.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS171.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS171.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.WS171.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS171.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS171.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:
----------------------------

       	WS171       	WS170      	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 23967)
------------------------------------------
Molecular_info              22274 (92.9%)
Concise_description          4401 (18.4%)
Reference                    6731 (28.1%)
CGC_approved Gene name       8945 (37.3%)
RNAi_result                 19843 (82.8%)
Microarray_results          19135 (79.8%)
SAGE_transcript             20061 (83.7%)




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

There are 20085 CDS in autoace, 23226 when counting 3141 alternate splice forms.

The 23226 sequences contain 10,187,058 base pairs in total.

Modified entries               6
Deleted entries                4
New entries                    3
Reappeared entries             3

Net change  +2



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   10745 (46.3%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4656 (20.0%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3489 (15.0%)
UniProtKB/TrEMBL accessions     19365 (83.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22854 (98.4%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   7303


GeneModel correction progress WS170 -> WS171
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     15  |     0  |
St Louis 	|     13  |     3  |
		+---------+--------+


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:
---------
C.remanei orthologs assignments are now made using the WashU preliminary gene set. 
Syntenic alignments of the genome sequence are still included in the compara download.

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

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


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


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


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



Model Changes:
------------------------------------
none

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


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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