Difference between revisions of "WS195"
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− | Status of entries: Protein_ID's in EMBL<br>---------------------------------------<br>Protein_id 23774 (99.4%)<br><br><br>Gene <-> CDS,Transcript,Pseudogene connections<br>----------------------------------------------<br>Caenorhabditis elegans entries with WormBase-approved Gene name 13924<br><br>GeneModel correction progress WS194 -> WS195<br>-----------------------------------------<br>Confirmed introns not in a CDS gene model;<br><br> +---------+--------+<br> | Introns | Change |<br> +---------+--------+<br>Cambridge | 27 | -83 |<br>St Louis | 103 | -55 |<br> +---------+--------+<br><br><br>Members of known repeat families that overlap predicted exons;<br><br> +---------+--------+<br> | Repeats | Change |<br> +---------+--------+<br>Cambridge | 6 | 0 |<br>St Louis | 6 | 0 |<br> +---------+--------+<br><br><br><br>Synchronisation with GenBank / EMBL:<br>------------------------------------<br><br>CHROMOSOME_I sequence AC024201<br>CHROMOSOME_III sequence U13019<br>CHROMOSOME_III sequence AC006605<br>CHROMOSOME_IV sequence AF067612<br>CHROMOSOME_IV sequence AC025715<br>CHROMOSOME_X sequence U41550<br>CHROMOSOME_X sequence AC084152<br><br>There are no gaps remaining in the genome sequence<br>---------------<br>For more info mail | + | Status of entries: Protein_ID's in EMBL<br>---------------------------------------<br>Protein_id 23774 (99.4%)<br><br><br>Gene <-> CDS,Transcript,Pseudogene connections<br>----------------------------------------------<br>Caenorhabditis elegans entries with WormBase-approved Gene name 13924<br><br>GeneModel correction progress WS194 -> WS195<br>-----------------------------------------<br>Confirmed introns not in a CDS gene model;<br><br> +---------+--------+<br> | Introns | Change |<br> +---------+--------+<br>Cambridge | 27 | -83 |<br>St Louis | 103 | -55 |<br> +---------+--------+<br><br><br>Members of known repeat families that overlap predicted exons;<br><br> +---------+--------+<br> | Repeats | Change |<br> +---------+--------+<br>Cambridge | 6 | 0 |<br>St Louis | 6 | 0 |<br> +---------+--------+<br><br><br><br>Synchronisation with GenBank / EMBL:<br>------------------------------------<br><br>CHROMOSOME_I sequence AC024201<br>CHROMOSOME_III sequence U13019<br>CHROMOSOME_III sequence AC006605<br>CHROMOSOME_IV sequence AF067612<br>CHROMOSOME_IV sequence AC025715<br>CHROMOSOME_X sequence U41550<br>CHROMOSOME_X sequence AC084152<br><br>There are no gaps remaining in the genome sequence<br>---------------<br>For more info mail help@wormbase.org<br>-===================================================================================-<br><br><br><br>New Data:<br>---------<br>C.JAPONICA<br>The C.japonica genome sequence and annotation are included in this release. <br>Gene predictions are from the nGASP project.<br>The standard set proteins sets have been blasted against the genome sequence and proteome.<br>Protein annotation with PFAM and InterPro domains etc is included.<br>Orthologies with other nematodes has been determined using the COMPARA analysis method and gene names transfered where appropriate.<br>C.japonica is also included in the multigenome alignments available from the FTP site.<br><br>Genome sequence updates:<br>-----------------------<br>NONE<br><br>New Fixes:<br>----------<br>A problem with CDSs that have more that one coding_transcipt being appearing as non-coding genes in the genome browser has been fixed. This was patched for WS194<br><br><br>Known Problems:<br>---------------<br><br><br>Other Changes:<br>--------------<br><br>Proposed Changes / Forthcoming Data:<br>-------------------------------------<br>The C.brenneri genome will be included in WS196<br><br><br>Model Changes:<br>------------------------------------<br><br>added confidence info to ?Interaction<br><br>fixed typo in ?Strain Phenotype_info<br><br>-===================================================================================-<br><br><br>Quick installation guide for UNIX/Linux systems<br>-----------------------------------------------<br><br>1. Create a new directory to contain your copy of WormBase,<br> e.g. /users/yourname/wormbase<br><br>2. Unpack and untar all of the database.*.tar.gz files into<br> this directory. You will need approximately 2-3 Gb of disk space.<br><br>3. Obtain and install a suitable acedb binary for your system<br> (available from www.acedb.org).<br><br>4. Use the acedb 'xace' program to open your database, e.g.<br> type 'xace /users/yourname/wormbase' at the command prompt.<br><br>5. See the acedb website for more information about acedb and<br> using xace.<br><br>____________ END _____________<br> |
= Patches = | = Patches = |
Latest revision as of 16:52, 21 December 2011
Release letter
New release of WormBase WS195, Wormpep195 and Wormrna195 Tue Sep 30 09:36:25 BST 2008
WS195 was built by Anthony
======================================================================
This directory includes:
i) database.WS195.*.tar.gz - compressed data for new release
ii) models.wrm.WS195 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS195-WS194.dbcomp - log file reporting difference from last release
v) wormpep195.tar.gz - full Wormpep distribution corresponding to WS195
vi) wormrna195.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS195.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS195.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix) gene_interpolated_map_positions.WS195.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS195.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS195.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.WS195.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS195.gz - list of all current gene identifiers with CGC & molecular names (when known)
xiv) PCR_product2gene.WS195.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:
----------------------------
WS195 WS194 change
----------------------------------------------
a 32365950 32365950 +0
c 17779889 17779889 +0
g 17756041 17756041 +0
t 32365753 32365753 +0
n 0 0 +0
- 0 0 +0
Total 100267633 100267633 +0
Chromosomal Changes:
--------------------
There are no changes to the chromosome sequences in this release.
Gene data set (Live C.elegans genes 29879)
------------------------------------------
Molecular_info 28159 (94.2%)
Concise_description 5443 (18.2%)
Reference 13229 (44.3%)
WormBase_approved Gene name 15596 (52.2%)
RNAi_result 0 (0%)
Microarray_results 20432 (68.4%)
SAGE_transcript 18844 (63.1%)
Wormpep data set:
----------------------------
There are 20198 CDS in autoace, 23906 when counting 3708 alternate splice forms.
The 23906 sequences contain 10,526,596 base pairs in total.
Modified entries 59
Deleted entries 34
New entries 55
Reappeared entries 0
Net change +21
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 8513 (35.6%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 10992 (46.0%) Some, but not all exon bases are covered by transcript evidence
Predicted 4401 (18.4%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions 23770 (99.4%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 23774 (99.4%)
Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name 13924
GeneModel correction progress WS194 -> WS195
-----------------------------------------
Confirmed introns not in a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 27 | -83 |
St Louis | 103 | -55 |
+---------+--------+
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_III sequence U13019
CHROMOSOME_III sequence AC006605
CHROMOSOME_IV sequence AF067612
CHROMOSOME_IV sequence AC025715
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:
---------
C.JAPONICA
The C.japonica genome sequence and annotation are included in this release.
Gene predictions are from the nGASP project.
The standard set proteins sets have been blasted against the genome sequence and proteome.
Protein annotation with PFAM and InterPro domains etc is included.
Orthologies with other nematodes has been determined using the COMPARA analysis method and gene names transfered where appropriate.
C.japonica is also included in the multigenome alignments available from the FTP site.
Genome sequence updates:
-----------------------
NONE
New Fixes:
----------
A problem with CDSs that have more that one coding_transcipt being appearing as non-coding genes in the genome browser has been fixed. This was patched for WS194
Known Problems:
---------------
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
-------------------------------------
The C.brenneri genome will be included in WS196
Model Changes:
------------------------------------
added confidence info to ?Interaction
fixed typo in ?Strain Phenotype_info
-===================================================================================-
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
Inparanoid
available at: [inparanoid_patch]
- as some C.elegans proteins in the Inparanoid6 XML files errouneoulsy specify Homo sapiens, some "dodgy" human proteins were created
- the patch should correct the ids, merge them into the C.elegans proteins and fix the Species + EnsEMBL xrefs