WS194

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Release Letter

New release of WormBase WS194, Wormpep194 and Wormrna194 Tue Sep  2 10:54:51 BST 2008


WS194 was built by Paul
======================================================================

This directory includes:
i)   database.WS194.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS194           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS194-WS193.dbcomp         -   log file reporting difference from last release
v)   wormpep194.tar.gz          -   full Wormpep distribution corresponding to WS194
vi)   wormrna194.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS194.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS194.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS194.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS194.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS194.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.WS194.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS194.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS194.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:
----------------------------

       	WS194       	WS193      	change
----------------------------------------------
a    	32365950	32365950	  +0
c    	17779889	17779890	  -1
g    	17756041	17756040	  +1
t    	32365753	32365752	  +1
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100267633	100267632	  +1

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

Chromosome: II
8971538 8971537 0   ->   8971538 8971538 1

Chromosome: IV
11046511 11046511 1   ->   11046511 11046510 0

Chromosome: V
10304795 10304794 0   ->   10304795 10304795 1


Gene data set (Live C.elegans genes 29882)
------------------------------------------
Molecular_info              28161 (94.2%)
Concise_description         5425 (18.2%)
Reference                   13190 (44.1%)
WormBase_approved Gene name 15564 (52.1%)
RNAi_result                 20818 (69.7%)
Microarray_results          20440 (68.4%)
SAGE_transcript             18844 (63.1%)




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

There are 20205 CDS in autoace, 23885 when counting 3680 alternate splice forms.

The 23885 sequences contain 10,505,526 base pairs in total.

Modified entries      85
Deleted entries       28
New entries           49
Reappeared entries    0

Net change  +21



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8492 (35.6%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10989 (46.0%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4404 (18.4%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  23749 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23753 (99.4%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  13892


GeneModel correction progress WS193 -> WS194
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|    110  |    80  |
St Louis 	|    158  |    13  |
		+---------+--------+


Members of known repeat families that overlap predicted exons;

		+---------+--------+
		| Repeats | Change |
		+---------+--------+
Cambridge	|      6  |     0  |
St Louis 	|      6  |     0  |
		+---------+--------+



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

CHROMOSOME_I	sequence AC024201
CHROMOSOME_II	sequence Z70034
CHROMOSOME_III	sequence AC087081
CHROMOSOME_III	sequence U13019
CHROMOSOME_III	sequence AC006605
CHROMOSOME_IV	sequence AF067612
CHROMOSOME_IV	sequence AC025715
CHROMOSOME_IV	sequence AC025724
CHROMOSOME_IV	sequence Z68760
CHROMOSOME_V	sequence Z71178
CHROMOSOME_X	sequence U41550
CHROMOSOME_X	sequence AC084152

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



New Data:
---------
The C.briggsae database has been rebuilt with some updated gene structures, orthology predictions and protein/transcript alignments.

Pristionchus pacificus is included for the first time including gene predictions imported from Ralf Sommer's group (paper in press).  We have 
calculated orthologies to C.elegans and transfered gene names where appropriate.
Further information available from http://wormbase.org/wiki/index.php/Pristionchus_pacificus

Genome sequence updates:
-----------------------
see above

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


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


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

Proposed Changes / Forthcoming Data:
-------------------------------------
C. japonica will be included in WS195, which will be the next frozen release.

We are working on calculating base pair conservation scores (using GERP) between the caenorhabditidae sp. elegans, briggsae, remanei, brenneri, and 
P.pacificus 
with Brugia malayi as an outgroup.  These are based on genome alignments and should be included in the near future.


Model Changes:
------------------------------------
Add a 'Non_directional' tag to the #Interaction_info hash, which will be used to list genes that are involved in non-directional interactions (e.g. 
synthetic).

Add to ?Evidence:
Mass_spec_evidence ?Mass_spec_peptide

Connect ?Strain and ?Phenotype

Add Name and Other_name to ?Feature

Change Gene.Ortholog_other to use Protein object rather than accessions

?Transgene changes to allow curation of transgene markers.

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


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 _____________

Patches

Protein Patches

Some data for proteins was missing (history,etc), the missing data can be found here for pristionchus and remanei.

Peptide Patches

The briggsae proteins were missing their peptide sequences, which can be found here