WormBase release WS153 now online
"WormBase" <[email protected]> Fri, 10 Feb 2006 21:58:10 -0500
| Newsgroups | gmane.science.biology.wormbase.announce,gmane.science.biology.wormbase.general |
|---|---|
| Message-ID | <[email protected]> |
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/WSWS153
New release of WormBase WS153, Wormpep153 and Wormrna153 Fri Jan 20 13:31:11 GMT 2006
WS153 was built by Gary
======================================================================
This directory includes:
i) database.WS153.*.tar.gz - compressed data for new release
ii) models.wrm.WS153 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS153-WS152.dbcomp - log file reporting difference from last release
v) wormpep153.tar.gz - full Wormpep distribution corresponding to WS153
vi) wormrna153.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS153.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS153.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS153.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS153.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS153.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.WS153.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS153.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS153.gz - Mappings between PCR products and overlapping Genes
Release notes on the web:
-------------------------
http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE
Primary databases used in build WS153
------------------------------------
brigdb : 2004-03-12
camace : 2006-01-04 - updated
citace : 2005-12-22 - updated
cshace : 2005-11-04
genace : 2006-01-04 - updated
stlace : 2005-12-22 - updated
Genome sequence composition:
----------------------------
WS153 WS152 change
----------------------------------------------
a 32365775 32366710 -935
c 17779813 17780365 -552
g 17755968 17756436 -468
t 32365578 32366406 -828
n 0 0 +0
- 0 0 +0
Total 100267134 100269917 -2783
(See the section 'New Fixes' below for an explanation of this change.)
Gene data set (Live C.elegans genes 23680)
------------------------------------------
Molecular_info 21927 (92.6%)
Concise_description 4131 (17.4%)
Reference 4884 (20.6%)
CGC_approved Gene name 8693 (36.7%)
RNAi_result 19769 (83.5%)
Microarray_results 19103 (80.7%)
SAGE_transcript 18197 (76.8%)
Wormpep data set:
----------------------------
There are 20057 CDS in autoace, 22901 when counting 2844 alternate splice forms.
The 22901 sequences contain 10,068,848 base pairs in total.
Modified entries 53
Deleted entries 38
New entries 36
Reappeared entries 2
Net change +0
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 6566 (28.7%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 11398 (49.8%) Some, but not all exon bases are covered by transcript evidence
Predicted 4937 (21.6%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions 3126 (13.7%)
UniProtKB/TrEMBL accessions 19443 (84.9%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 22569 (98.6%)
Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name 7002
GeneModel correction progress WS152 -> WS153
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 136 | -12 |
St Louis | 6 | -1 |
+---------+--------+
Members of known repeat families that overlap predicted exons;
+---------+--------+
| Repeats | Change |
+---------+--------+
Cambridge | 590 | 0 |
St Louis | 764 | -2 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
No synchronisation issues
There are no gaps remaining in the genome sequence
---------------
For more info mail [email protected]
-===================================================================================-
New Data:
---------
New Gene classes from James Thomas:
- math MATH (meprin-associated Traf homology) domain containing
- 50 genes added to class.
- fbxa F-box A protein
- 137 genes added to class
- fbxb F-box B protein
- 119 genes added to class
Updated homology data from ipi_human.
New Fixes:
----------
We had a sequence correction.
196 bases were removed from the beginning of C24G6, and what also will
seem like a deletion is that the overlap between T05C3 and C24G6 used
to be 200, but the true overlap was finished in both clones so the
actual overlap is now 2787.
Known Problems:
--------------
None.
Other Changes:
--------------
The Species of the EST query sequence has been added to the results of
BLAT searches by non-C.elegans ESTs (BLAT_NEMATODE, BLAT_WASHU and
BLAT_NEMBASE) in the CHROMOSOME_*.gff files.
Proposed Changes / Forthcoming Data:
------------------------------------
A forthcoming change to the model is:
Remove Interpolated_map_position from ?CDS, ?Transcript and ?Pseudogene.
Change ?Variation Interpolated_map_position to be same structure as ?Gene i.e.
Interpolated_map_position UNIQUE ?Map UNIQUE Float
Model Changes:
------------------------------------
URL Text added to following Classes:
Laboratory - to link to Lab homepage
Journal - to link to Journal homepage
Clone - to link to MRC_geneservice homepage (cant construct links to individual clones)
Microarray - to link to manufacturers site
To make use of the new ?Database base URL construction methods ?RNAi
and ?Variation have had DB_info lines added i.e.
?Variation / ?RNAi
DB_info Database ?Database ?Database_field UNIQUE ?Accession_no
For a better Transposon model an improved hierarchical structure has
been developed.
Transposon objects will be Smapped to a genomic clone and be named
WBTransposon000000. These will have Transposon_CDS S-children mapped
to them. This means that no Transposon_CDS will map directly to the
genome, but always via a transposon object.
Updated line in ?Transposon model Transposon repaces Sequence
S_child CDS_child ?CDS XREF Transposon UNIQUE Int UNIQUE Int #SMap_info
And in the ?CDS class
SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF CDS_child
Transposon UNIQUE ?Transposon XREF CDS_child <---- new line for Transposon conncetion
?Transposon_family is now also linked to ?Motif so that RepeatMasker
and PFAM etc domains related to Transposons can be connected.
-===================================================================================-
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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