WS216

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Release Letter

New release of WormBase WS216, Wormpep216 and Wormrna216 Tue Jun 29 12:53:35 BST 2010


WS216 was built by [Michael Paulini]
======================================================================

This directory includes:
i)   database.WS216.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS216           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS216-WS215.dbcomp         -   log file reporting difference from last release
v)   wormpep216.tar.gz          -   full Wormpep distribution corresponding to WS216
vi)   wormrna216.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS216.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS216.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS216.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS216.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS216.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.WS216.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS216.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS216.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:
----------------------------

       	WS216       	WS215      	change
----------------------------------------------
a    	32367418	32367418	  +0
c    	17780787	17780787	  +0
g    	17756985	17756985	  +0
t    	32367086	32367086	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100272276	100272276	  +0


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


Gene data set (Live C.elegans genes 40162)
------------------------------------------
Molecular_info              38477 (95.8%)
Concise_description         5666 (14.1%)
Reference                   14028 (34.9%)
WormBase_approved Gene name 25983 (64.7%)
RNAi_result                 22924 (57.1%)
Microarray_results          21070 (52.5%)
SAGE_transcript             19141 (47.7%)




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

There are 20364 CDS in autoace, 24652 when counting 4288 alternate splice forms.

The 24652 sequences contain 10,865,930 base pairs in total.

Modified entries      23
Deleted entries       26
New entries           79
Reappeared entries    3

Net change  +56




Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed             10131 (41.1%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11781 (47.8%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2740 (11.1%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  24474 (99.3%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            24475 (99.3%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24346


GeneModel correction progress WS215 -> WS216
-----------------------------------------
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:
------------------------------------

CHROMOSOME_I	sequence AC024794
CHROMOSOME_I	sequence AF067219
CHROMOSOME_II	sequence AF025454
CHROMOSOME_II	sequence U49955
CHROMOSOME_II	sequence U23519
CHROMOSOME_II	sequence U41278
CHROMOSOME_II	sequence U29244
CHROMOSOME_II	sequence U39999
CHROMOSOME_III	sequence U00057
CHROMOSOME_III	sequence U23514
CHROMOSOME_III	sequence U50193
CHROMOSOME_III	sequence U23177
CHROMOSOME_III	sequence AC006679
CHROMOSOME_III	sequence L16621
CHROMOSOME_IV	sequence AF038604
CHROMOSOME_IV	sequence U97593
CHROMOSOME_V	sequence AF024503
CHROMOSOME_X	sequence U41553
CHROMOSOME_X	sequence U39653
CHROMOSOME_X	sequence U64859
CHROMOSOME_X	sequence U39741
CHROMOSOME_X	sequence AC199239

There are no gaps remaining in the genome sequence
---------------
For more info mail help@wormbase.org
-===================================================================================-



New Data:
---------
* new Pristionchus gene curation:
       changes to 17 genes used in Pristionchus publications

* Brugia gene set refinement:
       further gene merges and isoform cleanups

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


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


Known Problems:
---------------
* three C.remanei CDSes don't have gene ids


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

Proposed Changes / Forthcoming Data:
-------------------------------------
* added Brief_id  to ?Position_Matrix class
* new ?Molecule class 

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 _____________

known bugs

confirmed introns

There seems to be a systematic 12bp shift in the confirmed intron features coming from RNAseq data - Removed for WS217

None of the Transcript confirmed intron data was processed for this build. - Resolved for WS217

missing C.remanei genes

There are three C.remanei CDSes that are missing gene ids

AGP

there are errors in the C.elegans AGP file (clones being out of sync with the public repositories), which will be solved in WS217.