WormBase release WS181 now online
"Todd Harris" <[email protected]> Sun, 30 Sep 2007 14:39:04 -0400
| Newsgroups | gmane.science.biology.wormbase.announce |
|---|---|
| Message-ID | <200709301839.l8UId4qq013304__42669.6139657453$1191177933$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/WSWS181
New release of WormBase WS181, Wormpep181 and Wormrna181 Fri Sep 7 11:40:20 BST 2007
WS181 was built by Gary Williams
======================================================================
This directory includes:
i) database.WS181.*.tar.gz - compressed data for new release
ii) models.wrm.WS181 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS181-WS180.dbcomp - log file reporting difference from last release
v) wormpep181.tar.gz - full Wormpep distribution corresponding to WS181
vi) wormrna181.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS181.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS181.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS181.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS181.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS181.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.WS181.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS181.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS181.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:
----------------------------
WS181 WS180 change
----------------------------------------------
a 32365949 32365949 +0
c 17779887 17779887 +0
g 17756036 17756036 +0
t 32365750 32365750 +0
n 0 0 +0
- 0 0 +0
Total 100267622 100267622 +0
Chromosomal Changes:
--------------------
There are no changes to the chromosome sequences in this release.
Gene data set (Live C.elegans genes 29501)
------------------------------------------
Molecular_info 27790 (94.2%)
Concise_description 4889 (16.6%)
Reference 7211 (24.4%)
CGC_approved Gene name 14732 (49.9%)
RNAi_result 20690 (70.1%)
Microarray_results 19945 (67.6%)
SAGE_transcript 18645 (63.2%)
Wormpep data set:
----------------------------
There are 20144 CDS in autoace, 23518 when counting 3374 alternate splice forms.
The 23518 sequences contain base pairs in total.
Modified entries 23
Deleted entries 0
New entries 11
Reappeared entries 0
Net change +11
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 8109 (34.5%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 10746 (45.7%) Some, but not all exon bases are covered by transcript evidence
Predicted 4663 (19.8%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions 3439 (14.6%)
UniProtKB/TrEMBL accessions 18829 (80.1%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 22278 (94.7%)
Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name 13107
GeneModel correction progress WS180 -> WS181
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 24 | 1 |
St Louis | 157 | -1 |
+---------+--------+
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 [email protected]
-===================================================================================-
New Data:
---------
The following BLAST databases were updated to the latest version:
gadfly
ipi_human
yeast
Genome sequence updates:
-----------------------
New Fixes:
----------
Known Problems:
---------------
Other Changes:
--------------
Analysis objects are now being used for evidence of orthologs.
Proposed Changes / Forthcoming Data:
-------------------------------------
2944 5' and 3' RACE sequences from the Vidal lab will be aligned to
the C.elegans genome giving an improved view of the ends of many
genes.
Proposed Model Changes
----------------------
Added History tracking tags to ?Feature class
Removed WashU_ID and Exelixis_ID as Variation name types
Added Amber_UAG_or_Opal_UGA as final ambiguous mutation
Model Changes:
------------------------------------
#####################################################################
#Molecular_change Nonsense UNIQUE Amber_UAG Text #Evidence
Ochre_UAA Text #Evidence
Opal_UGA Text #Evidence
Ochre_UAA_or_Opal_UGA Text #Evidence
Amber_UAG_or_Ochre_UAA Text #Evidence
######################################################################
?Transcript
Properties Transcript mRNA
miRNA
ncRNA
rRNA
scRNA
snRNA
snlRNA *new Small Nuclear Like RNA
snoRNA
stRNA
tRNA
u21RNA
#################################################################################################
#Splice_confirmation cDNA ?Sequence // ?Sequence link to flag which cDNA is confirming
EST ?Sequence // or falsifying the intron in question, added [031121 krb]
OST
mRNA
Homology
UTR ?Sequence
False ?Sequence
Inconsistent ?Sequence
#################################################################################################
// the main Analysis class To hold information about Publications / Persons / other evidence and the used WormBase Release
?Analysis Source_database ?Database
Based_on_WB_Release Int
Based_on_DB_Release Text
Description ?Text
Reference ?Paper XREF Describes_analysis
Conducted_by ?Person XREF Describes_analysis // not always the same as the author of the paper - eg Erich running OrthoMCL
URL Text // eg www.treefam.org (or would this be covered by Source_database?)
// changes to the Evidence
#Evidence From_analysis ?Analysis
// Paper class changes
?Paper Describes_analysis ?Analysis XREF Reference
// Person class changes
?Person Conducted ?Analysis XREF Conducted_by
-===================================================================================-
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 _____________