WormBase release WS177 now online
"Todd Harris" <[email protected]> Wed, 11 Jul 2007 18:01:31 -0400
| Newsgroups | gmane.science.biology.wormbase.announce |
|---|---|
| Message-ID | <200707112201.l6BM1VuJ018919__2796.37009739435$1184191438$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/WSWS177
New release of WormBase WS177, Wormpep177 and Wormrna177 Fri Jun 15 15:39:40 BST 2007
WS177 was built by Michael Han
======================================================================
This directory includes:
i) database.WS177.*.tar.gz - compressed data for new release
ii) models.wrm.WS177 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS177-WS176.dbcomp - log file reporting difference from last release
v) wormpep177.tar.gz - full Wormpep distribution corresponding to WS177
vi) wormrna177.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS177.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS177.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS177.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS177.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS177.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.WS177.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS177.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS177.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:
----------------------------
WS177 WS176 change
----------------------------------------------
a 32365888 32365889 -1
c 17779856 17779856 +0
g 17756017 17756016 +1
t 32365689 32365689 +0
Total 100267450 100267450
Chromosomal Changes:
--------------------
Chromosome: I
7301405 7301404 0 -> 7301405 7301405 1
9606432 9606431 0 -> 9606433 9606433 1
Chromosome: III
9778413 9778413 1 -> 9778413 9778412 0
9863640 9863639 0 -> 9863639 9863639 1
Chromosome: V
10766209 10766209 1 -> 10766209 10766208 0
Chromosome: X
11848274 11848274 1 -> 11848274 11848273 0
Gene data set (Live C.elegans genes 24123)
------------------------------------------
Molecular_info 22418 (92.9%)
Concise_description 4732 (19.6%)
Reference 7097 (29.4%)
CGC_approved Gene name 9279 (38.5%)
RNAi_result 19875 (82.4%)
Microarray_results 19569 (81.1%)
SAGE_transcript 0 (0%)
Wormpep data set:
----------------------------
There are 20140 CDS in autoace, 23412 when counting 3272 alternate splice forms.
The 23412 sequences contain 10,288,612 base pairs in total.
Modified entries 52
Deleted entries 0
New entries 62
Reappeared entries 2
Net change +64
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 8020 (34.3%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 10747 (45.9%) Some, but not all exon bases are covered by transcript evidence
Predicted 4645 (19.8%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions 3544 (15.1%)
UniProtKB/TrEMBL accessions 19448 (83.1%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 22992 (98.2%)
Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name 7641
GeneModel correction progress WS176 -> WS177
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 0 | -70 |
St Louis | 0 | -179 |
+---------+--------+
Members of known repeat families that overlap predicted exons;
+---------+--------+
| Repeats | Change |
+---------+--------+
Cambridge | 0 | -6 |
St Louis | 0 | -6 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
CHROMOSOME_V sequence Z72508
CHROMOSOME_X sequence Z67755
There are no gaps remaining in the genome sequence
---------------
For more info mail [email protected]
-===================================================================================-
New Data:
---------
New orthology data from user submissions was added and curated.
EnsEMBL orthologues from EnsEMBL-compara release 44 were imported to update the ortholog_other EnsEMBL data.
Large increases of Anatomy_term and Anatomy_name have been made in order to clearly distinguish the identity of a cell (e.g. ABalapp) from its nucleus (e.g. ABalapp nucleus).
Transcript alignment data from non C.elegans Caenorhabditis species (C.briggsae / C. brenneri / C.remanei / C.japonica) to the C.elegans genome was added to WormBase.
Genome sequence updates:
-----------------------
7 changes were made to the genome sequence:
F54F7 deletion tagctcaccagcttgcacgGgaagtgaaagtcttgaaata
F28H7 deletion aacaaaatcttgcaactagTaatgtgaaaaagtgtggact
K07A1 insertion ttctcaaatttcagtttatTggaacattacaaatatgtgt
F13G3 insertion tttttttcagacaccgttcgtttggctccgGcgcgatcaacatggtgatggttgcacaagg
R10E11 deletion gccacctggaaatcaatcagctcctcaaaaAgaattccgaatctgcctatattctgttcta
K11H3 insertion gcattaacaacacacggaaatcgaaatggaCcacttcgttatagtcttcttcaacaacgag
Y95D11A shift-overlap GTTATATATTTTTTTGGAAATTTATAACTCTTAAAAAAATTCAATTTTTTCAAATAAATAAAATTTCAGATGGCTTCTCAACCGGAGCTCATAATGGTTG
ACGAGCAAGTCGTCGCTTATGAAGTAGAAATTGATAGTTTTGATGTAAAATATGATGAAGAGGAACATGATGGTCAAGGGACACAAGATGAACCATTTTC
TCATGGTACGGAACAGTTTTACGCTGAAAAATTCCAGAATTCCAAAAAATGAAACCTAAAATAGTGATAAAAAGGCGTTTTGAATATTAAATTGAAGAAA
AAAATCAGCAAAAATTGTTCAAAATCAAGAATTTTAACGGAAAAGTGTAAAATCTTCTCCACGGGGAGTACACATGCTTCGTAAATCGACATATGGTCAA
TTTTAAAGTTTTGAAAATTGAAATGCCGGCAAAAAATCTTTTCTTGTTTTTTTTTCGCAAAAAATTCAATTTTCGAAAAAATAATTATAGAAAATTGCAT
TTTTTGACCGAAAAGTCAATAAAAATAACAGAAAAAATCGATAAACCGTTGAAAAATTTTTTTTTAATTCAAAAATTCAGAAATTCTTAAAATTCAAATT
TCCAGATGAGCCAAGCACCAGCGGTTATCACCATCACTACCAATTTCCCAATGACGTGGATCCAAATGATGTTTATTTATTCGATGAGGTATCAATTATC
CGAAATTTGGCGATTTTTGAGCCAAAACTACGGTACCCGGTCTCGACACGACAATTTTTGTTAAATTAAAAAAGGTGTGCGCCTTTGAAGGTTACTGTAG
TTTCGAACTTTTGCTGATTTTTCATATTTTTTCGTTGAAAACAAAAGTATTTATTTGTTGAAAATCAGAAAATATTATCTTCGCGTCGAGACCTATTACC
ATTCTATTTTTGCCGCAAAAAACAAAATTTCCTTTAAAAAAAAGCTAATTTTTCCAAGTTTTTCCAGGAAACTGATCAAATTCATCAGCTCGACCCGAAT
CAACTCAAAAATAATGAAGAAATTGACGATGTCGAATATATTGATCAATCTGTGCCTTCCACGTCATCAATGATGACGTCACTGCCGTCAACGGTGGCTC
CAGTTCAGCCAAATACGTATTACAGACGGAAATCTGGAGGCCCAACTGCAACTGGAAATGAAAAACCGAATTATAGGCCGTTGGCGTTCCAAACGGTTCG
taaaataaaaaaaatgtccatgtgtcgatt
New Fixes:
----------
Known Problems:
---------------
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
-------------------------------------
Additional genome changes are planned for WS178.
Model Changes:
------------------------------------
-===================================================================================-
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 _____________