WormBase release WS110 now online

This is an automatic announcement that WormBase
(http://www.wormbase.org) has just been updated.  New releases occur
roughly every 2 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/

New release of WormBase WS110, Wormpep110 and Wormrna110 Mon Sep 22 09:58:44 BST 2003


WS110 was built by Chao-Kung Chen  
======================================================================

This directory includes:
i)	database.WS110.*.tar.gz    -   compressed data for new release
ii)	models.wrm.WS110           -   the latest database schema (also in above database files)
iii)	CHROMOSOMES/subdir        -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)	WS110-WS109.dbcomp          -   log file reporting difference from last release
v)	wormpep110.tar.gz          -   full Wormpep distribution corresponding to WS110
vi)	wormrna110.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)	confirmed_genes.WS110.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii)	yk2orf.WS110.gz            -    Latest set of ORF connections to each Yuji Kohara EST clone
ix)	gene_interpolated_map_positions.WS110.gz    - Interpolated map positions for each coding/RNA gene
x)	clone_interpolated_map_positions.WS110.gz    - Interpolated map positions for each clone
xi)	best_blastp_hits.WS110.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.WS110.gz   - for each C. briggsae protein, lists Best blastp match to
 
                                        human, fly, yeast, C. elegans, and SwissProt & Trembl proteins.


Release notes on the web:
-------------------------
http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE



Primary databases used in build WS110
------------------------------------
brigdb : 2003-09-08 - updated
camace : 2003-09-09 - updated
citace : 2003-09-07 - updated
cshace : 2003-09-04 - updated
genace : 2003-09-16 - updated
stlace : 2003-09-08 - updated


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

       	WS110       	WS109      	change
----------------------------------------------
a    	32367165	32367165	  +0
c    	17780236	17780236	  +0
g    	17757587	17757587	  +0
t    	32368413	32368413	  +0
n    	95      	95      	  +0
-    	0       	0       	  +0

Total	100273496	100273496	  +0




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

There are 19936 CDS in autoace, 22168 when counting 2232 alternate splice forms.

The 22168 sequences contain 9,672,725 base pairs in total.

Modified entries             291
Deleted entries               35
New entries                   73
Reappeared entries             2

Net change  +40



Status of entries: Confidence level of prediction
-------------------------------------------------
Confirmed              4589 (20.7%)
Partially_confirmed    9040 (40.8%)
Predicted              8527 (38.5%)



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2413 (10.9%)
TrEMBL accessions     18085 (81.6%)
TrEMBLnew accessions   1650 (7.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22148 (100.0%)



Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection   4460


GeneModel correction progress WS109 -> WS110
-----------------------------------------
Confirmed introns not is a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|      6  |  -1056  |
St Louis 	|     40  |  -710  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     30  |     1  |
St Louis 	|     31  |     0  |
		+---------+--------+



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

No synchronisation issues


There are no gaps remaining in the genome sequence
---------------
For more info mail [email protected]
-===================================================================================-

NOTE:
-----

This release (WS110) is the second frozen release followed WS100.
It represents a freeze-of-data release and will remain on the Sanger ftp site 
(ftp://ftp.sanger.ac.uk/pub/wormbase) for the foreseeable future.
Also, it will be available from http://ws110.wormbase.org

Bioinformaticians seeking to collaborate and share annotation data against the backdrop of a fixed
genome sequence may consider working with this release.

The next freeze will take place with the release of WS120, approximately in 20 weeks time

Please address any queries to [email protected]

New Data:
---------
- New Briggsae protein set brigpep2

- C.elegans BlastP/X results against brigpep2
- C.briggsae BLASTP against C.elegans, human, fly, yeast, SWALL

- Using latest BLAT binary and optimised BLAT BEST/OTHER output for 
  C.elegans ESTs (and Marc Vidal OSTs)
  C.elegans mRNAs
  Other nematode ESTs
  Non-Wormbase GenBank/EMBL C. elegans CDS sequence submissions


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

The optimization of BLAT dataset improves identifying scoring best BLAT results for OSTs, ESTs, mRNAs, etc.

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

- Some SNP data and a few transcript objects were missing, and will be fixed     
  in the next regular release.

- Missing sequence features like SL2 and will be included in the next release

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

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

- tRNA predictions will be updated using latest tRNASCAN-SE-1.23 for WS112.

- Ongoing optimization for validating evidences supporting gene models.

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


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 _____________