https://wiki.wormbase.org/index.php?title=WS207&feed=atom&action=history
WS207 - Revision history
2024-03-29T05:52:44Z
Revision history for this page on the wiki
MediaWiki 1.33.0
https://wiki.wormbase.org/index.php?title=WS207&diff=13227&oldid=prev
Pdavis at 16:42, 21 December 2011
2011-12-21T16:42:18Z
<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<col class="diff-marker" />
<col class="diff-content" />
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 16:42, 21 December 2011</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l117" >Line 117:</td>
<td colspan="2" class="diff-lineno">Line 117:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There are no gaps remaining in the genome sequence</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There are no gaps remaining in the genome sequence</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>---------------</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>---------------</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>For more info mail <del class="diffchange diffchange-inline">worm</del>@<del class="diffchange diffchange-inline">sanger</del>.<del class="diffchange diffchange-inline">ac.uk</del></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>For more info mail <ins class="diffchange diffchange-inline">help</ins>@<ins class="diffchange diffchange-inline">wormbase</ins>.<ins class="diffchange diffchange-inline">org</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>-===================================================================================-</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>-===================================================================================-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
</table>
Pdavis
https://wiki.wormbase.org/index.php?title=WS207&diff=2986&oldid=prev
Mh6: added a patch for dodgy protein homologies and proteins
2009-10-08T11:31:00Z
<p>added a patch for dodgy protein homologies and proteins</p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 11:31, 8 October 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">= Release Notes =</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><pre></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><pre></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>New release of WormBase WS207, Wormpep207 and Wormrna207 Mon Sep 28 11:47:26 BST 2009</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>New release of WormBase WS207, Wormpep207 and Wormrna207 Mon Sep 28 11:47:26 BST 2009</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l182" >Line 182:</td>
<td colspan="2" class="diff-lineno">Line 183:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></pre></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></pre></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">= Patches =</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">== Protein ==</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Some proteins have additional zombie proteins in their blast homology data. A patch to fix that is at ftp://ftp.sanger.ac.uk/pub2/wormbase/WS207/acedb/protein_patch.ace</ins></div></td></tr>
</table>
Mh6
https://wiki.wormbase.org/index.php?title=WS207&diff=2947&oldid=prev
Pdavis at 03:58, 29 September 2009
2009-09-29T03:58:51Z
<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 03:58, 29 September 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><pre></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>New release of WormBase WS207, Wormpep207 and Wormrna207 Mon Sep 28 11:47:26 BST 2009</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>New release of WormBase WS207, Wormpep207 and Wormrna207 Mon Sep 28 11:47:26 BST 2009</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l179" >Line 179:</td>
<td colspan="2" class="diff-lineno">Line 180:</td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>____________ END _____________</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>____________ END _____________</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></pre></ins></div></td></tr>
</table>
Pdavis
https://wiki.wormbase.org/index.php?title=WS207&diff=2946&oldid=prev
Pdavis: New page: New release of WormBase WS207, Wormpep207 and Wormrna207 Mon Sep 28 11:47:26 BST 2009 WS207 was built by Paul Davis ======================================================================...
2009-09-29T03:58:21Z
<p>New page: New release of WormBase WS207, Wormpep207 and Wormrna207 Mon Sep 28 11:47:26 BST 2009 WS207 was built by Paul Davis ======================================================================...</p>
<p><b>New page</b></p><div>New release of WormBase WS207, Wormpep207 and Wormrna207 Mon Sep 28 11:47:26 BST 2009<br />
<br />
<br />
WS207 was built by Paul Davis<br />
======================================================================<br />
<br />
This directory includes:<br />
i) database.WS207.*.tar.gz - compressed data for new release<br />
ii) models.wrm.WS207 - the latest database schema (also in above database files)<br />
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)<br />
iv) WS207-WS206.dbcomp - log file reporting difference from last release<br />
v) wormpep207.tar.gz - full Wormpep distribution corresponding to WS207<br />
vi) wormrna207.tar.gz - latest WormRNA release containing non-coding RNA's in the genome<br />
vii) confirmed_genes.WS207.gz - DNA sequences of all genes confirmed by EST &/or cDNA<br />
viii) cDNA2orf.WS207.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)<br />
ix) gene_interpolated_map_positions.WS207.gz - Interpolated map positions for each coding/RNA gene<br />
x) clone_interpolated_map_positions.WS207.gz - Interpolated map positions for each clone<br />
xi) best_blastp_hits.WS207.gz - for each C. elegans WormPep protein, lists Best blastp match to<br />
human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins.<br />
xii) best_blastp_hits_brigprot.WS207.gz - for each C. briggsae protein, lists Best blastp match to<br />
human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.<br />
xiii) geneIDs.WS207.gz - list of all current gene identifiers with CGC & molecular names (when known)<br />
xiv) PCR_product2gene.WS207.gz - Mappings between PCR products and overlapping Genes<br />
<br />
<br />
Release notes on the web:<br />
-------------------------<br />
http://www.wormbase.org/wiki/index.php/Release_Schedule<br />
<br />
<br />
<br />
Genome sequence composition:<br />
----------------------------<br />
<br />
WS207 WS206 change<br />
----------------------------------------------<br />
a 32367418 32367418 +0<br />
c 17780763 17780763 +0<br />
g 17756943 17756943 +0<br />
t 32367086 32367086 +0<br />
n 0 0 +0<br />
- 0 0 +0<br />
<br />
Total 100272210 100272210 +0<br />
<br />
<br />
Chromosomal Changes:<br />
--------------------<br />
There are no changes to the chromosome sequences in this release.<br />
<br />
<br />
Gene data set (Live C.elegans genes 39985)<br />
------------------------------------------<br />
Molecular_info 38279 (95.7%)<br />
Concise_description 4925 (12.3%)<br />
Reference 13643 (34.1%)<br />
WormBase_approved Gene name 25839 (64.6%)<br />
RNAi_result 22830 (57.1%)<br />
Microarray_results 21055 (52.7%)<br />
SAGE_transcript 19046 (47.6%)<br />
<br />
<br />
<br />
<br />
Wormpep data set:<br />
----------------------------<br />
<br />
There are 20231 CDS in autoace, 24185 when counting 3954 alternate splice forms.<br />
<br />
The 24185 sequences contain 10,689,789 base pairs in total.<br />
<br />
Modified entries 146<br />
Deleted entries 25<br />
New entries 67<br />
Reappeared entries 3<br />
<br />
Net change +45<br />
The differnce between the total CDS's of this (24185) and the last build (24143) does not equal the net change 45<br />
Please investigate! ! <br />
<br />
<br />
<br />
<br />
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)<br />
-------------------------------------------------<br />
Confirmed 9819 (40.6%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 11573 (47.9%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 2793 (11.5%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Status of entries: Protein Accessions<br />
-------------------------------------<br />
UniProtKB accessions 24045 (99.4%)<br />
<br />
<br />
<br />
Status of entries: Protein_ID's in EMBL<br />
---------------------------------------<br />
Protein_id 24045 (99.4%)<br />
<br />
<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Caenorhabditis elegans entries with WormBase-approved Gene name 24181<br />
<br />
<br />
Synchronisation with GenBank / EMBL:<br />
------------------------------------<br />
<br />
No synchronisation issues<br />
<br />
<br />
There are no gaps remaining in the genome sequence<br />
---------------<br />
For more info mail worm@sanger.ac.uk<br />
-===================================================================================-<br />
<br />
<br />
<br />
New Data:<br />
---------<br />
Duplicon region features from paper WBPaper00034747<br />
http://www.wormbase.org/db/misc/paper?name=WBPaper00034747;class=Paper<br />
WBsf038821 - WBsf042304<br />
<br />
HTZ-1 binding site regions added WBPaper00032180<br />
http://www.wormbase.org/db/misc/paper?name=WBPaper00032180;class=Paper<br />
WBsf042314 - WBsf047477<br />
<br />
Genome sequence updates:<br />
-----------------------<br />
<br />
<br />
New Fixes:<br />
----------<br />
<br />
Longtext EST/mRNA patched<br />
70,000 Sequence entries were missing their EMBL/GENBANK accession info inm <br />
previous releases.<br />
<br />
<br />
Known Problems:<br />
---------------<br />
<br />
<br />
Other Changes:<br />
--------------<br />
<br />
Proposed Changes / Forthcoming Data:<br />
-------------------------------------<br />
<br />
<br />
Model Changes:<br />
------------------------------------<br />
<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 _____________</div>
Pdavis