WormBase release WS159 now online
"WormBase" <[email protected]> Wed, 21 Jun 2006 01:16:57 -0400
| Newsgroups | gmane.science.biology.wormbase.announce |
|---|---|
| Message-ID | <200606210516.k5L5GveL005002__5047.92657816342$1150867269$gmane$org@brie6.cshl.edu> |
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/WSWS159
New release of WormBase WS159, Wormpep159 and Wormrna159 Thu May 25 14:14:24 BST 2006
WS159 was built by [INSERT NAME HERE]
======================================================================
This directory includes:
i) database.WS159.*.tar.gz - compressed data for new release
ii) models.wrm.WS159 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS159-WS158.dbcomp - log file reporting difference from last release
v) wormpep159.tar.gz - full Wormpep distribution corresponding to WS159
vi) wormrna159.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS159.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS159.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS159.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS159.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS159.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.WS159.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS159.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS159.gz - Mappings between PCR products and overlapping Genes
Release notes on the web:
-------------------------
http://wwwdev.sanger.ac.uk/Projects/C_elegans/WORMBASE
Genome sequence composition:
----------------------------
WS159 WS158 change
----------------------------------------------
a 32365888 32365775 +113
c 17779855 17779813 +42
g 17756011 17755968 +43
t 32365687 32365578 +109
n 0 0 +0
Total 100267441 100267134 +307
Total number of bases has increased.
Chromosomal Changes:
--------------------
Chromosome: II
9225832 9225831 0 -> 9225832 9225832 1
Chromosome: III
3837845 3837844 0 -> 3837845 3837845 1
12723210 12723225 16 -> 12723211 12723228 18
12924804 12924803 0 -> 12924807 12925163 357
Chromosome: V
20248195 20248327 133 -> 20248195 20248273 79
These are the altered clones for WS159
--------------------------------------
--------------------------------------------------------
Chrom Clone start size and type
--------------------------------------------------------
5 Y113G7B 65346 54bp deletion
2 ZK1067 41275 1bp insertion
3 C36A4 9281 1bp insertion
3 Y37D8A 108017 357bp insertion
3 Y111B2A 230446 230465 2x1bp insertions
Gene data set (Live C.elegans genes 23750)
------------------------------------------
Molecular_info 22006 (92.7%)
Concise_description 4178 (17.6%)
Reference 5835 (24.6%)
CGC_approved Gene name 8781 (37%)
RNAi_result 19794 (83.3%)
Microarray_results 19124 (80.5%)
SAGE_transcript 18180 (76.5%)
Wormpep data set:
----------------------------
There are 20095 CDS in autoace, 23170 when counting 3075 alternate splice forms.
The 23170 sequences contain 10,170,801 base pairs in total.
Modified entries 10
Deleted entries 9
New entries 16
Reappeared entries 1
Net change +8
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 6695 (28.9%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 11442 (49.4%) Some, but not all exon bases are covered by transcript evidence
Predicted 5033 (21.7%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions 3220 (14.0%)
UniProtKB/TrEMBL accessions 19687 (85.9%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 22907 (98.9%)
Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name 7093
GeneModel correction progress WS158 -> WS159
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 22 | -3271 |
St Louis | 6 | -9 |
+---------+--------+
The change of -3271 is mostly a result of fixing a problem in the previous version.
Members of known repeat families that overlap predicted exons;
+---------+--------+
| Repeats | Change |
+---------+--------+
Cambridge | 584 | 6 |
St Louis | 750 | 0 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
There are no gaps remaining in the genome sequence
---------------
For more info mail [email protected]
-===================================================================================-
New Data:
---------
Phenotype objects have undergone a very large increase for this
release -- from 128 objects to 1253 objects, reflecting the release of
the phenotype ontology. The new phenotype objects will coexist with
the old (soon to be deprecated) phenotype objects for the time-being.
RNAi objects for this release are annotated with both old and new
phenotypes, so RNAi objects will have the current style annotations
with short names (e.g. Adl, Let, Bli) and will also be linked to
WBPhenotype objects. The release of the phenotype ontology correlates
with significant changes to the #Phenotype_info, ?Phenotype, and
?Variation models (though the old tags in ?Variation will coexist with
the new tags in #Phenotype_info for now), and there is a new
?Phenotype_name model.
98 Paper objects corresponding to WormBook chapters have been added to
WormBase. They contain citation information as well as lists of gene,
cell, variation, clone, transgene and rearrangement objects discussed
in a particular chapter. This will allow us to provide direct links to
WormBook from Paper, Gene and other WormBase pages.
New Fixes:
----------
Known Problems:
--------------
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
------------------------------------
Model Changes:
------------------------------------
* Added Homo_homol to Expr_pattern for Wen.
* Changes to Anatomy_term to allow movement of data from cell and
cell_group classes.
* Minor alterations for Carol's Phenotype update.
* Made Phenotype related changes, leaving in transitionary tags to hold
data until Caltech are ready to complete transfer.
-===================================================================================-
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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