WS186

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Release Notes

New release of WormBase WS186, Wormpep186 and Wormrna186 Fri Dec 21 08:57:59 GMT 2007


WS186 was built by Mary Ann (mt3@sanger.ac.uk)
======================================================================

This directory includes:
i)   database.WS186.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS186           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS186-WS185.dbcomp         -   log file reporting difference from last release
v)   wormpep186.tar.gz          -   full Wormpep distribution corresponding to WS186
vi)   wormrna186.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS186.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS186.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS186.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS186.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS186.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.WS186.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS186.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS186.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:
----------------------------

       	WS186       	WS185      	change
----------------------------------------------
a    	32365950	32365949	  +1
c    	17779886	17779887	  -1
g    	17756037	17756036	  +1
t    	32365750	32365750	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100267623	100267622	  +1

Chromosomal Changes:
--------------------

Chromosome: II
8655100 8655100 1   ->   8655100 8655100 1

Chromosome: X
14718205 14718204 0   ->   14718205 14718205 1


Gene data set (Live C.elegans genes 29624)
------------------------------------------
Molecular_info              27922 (94.3%)
Concise_description         5074 (17.1%)
Reference                   7523 (25.4%)
WormBase_approved Gene name 15141 (51.1%)
RNAi_result                 20733 (70%)
Microarray_results          19959 (67.4%)
SAGE_transcript             18722 (63.2%)




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

There are 20169 CDS in autoace, 23645 when counting 3476 alternate splice forms.

The 23645 sequences contain  base pairs in total.

Modified entries      83
Deleted entries       30
New entries           48
Reappeared entries    3

Net change  +21



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8316 (35.2%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10966 (46.4%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4363 (18.5%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3644 (15.4%)
UniProtKB/TrEMBL accessions      19604 (82.9%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23248 (98.3%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  13490


GeneModel correction progress WS185 -> WS186
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    124  |    65  |
St Louis 	|    472  |    27  |
		+---------+--------+


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 worm@sanger.ac.uk
-===================================================================================-



New Data:
---------


Genome sequence updates:
-----------------------
F33C8    insertion   catgctaagccaattctcatcggccggagGtccaacacctctatccatcgaaccgtgtag
D2085    deletion    cactttcagaatcgctgaagcatttaatgtcaCcggacctttcaatatgcagctcattgctaaaaataacga
D2085    insertion   cactttcagaatcgctgaagcatttaatgtcaAcggacctttcaatatgcagctcattgctaaaaataacga 

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


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


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

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


Model Changes:
------------------------------------
Removed the Microarray_results tag from the ?Microarray class and consequently the 
XREF between ?Microarray_results and ?Microarray classes.

?Microarray_results class will still have a link to ?Microarray.
The reason for that is that AceDB begins to struggle when one object is linked to 
very many, which is the case for some (notably tiling) arrays.
-===================================================================================-


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.