https://wiki.wormbase.org/index.php?title=WS229&feed=atom&action=history
WS229 - Revision history
2024-03-29T11:12:43Z
Revision history for this page on the wiki
MediaWiki 1.33.0
https://wiki.wormbase.org/index.php?title=WS229&diff=13202&oldid=prev
Pdavis at 11:15, 21 December 2011
2011-12-21T11:15:59Z
<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<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 11:15, 21 December 2011</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l459" >Line 459:</td>
<td colspan="2" class="diff-lineno">Line 459:</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;"></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="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=WS229&diff=12976&oldid=prev
Matuli: /* DB_remarks */
2011-12-08T16:07:11Z
<p><span dir="auto"><span class="autocomment">DB_remarks</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<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 16:07, 8 December 2011</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l486" >Line 486:</td>
<td colspan="2" class="diff-lineno">Line 486:</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>=== Bug Fixes ===</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>=== Bug Fixes ===</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>==== DB_remarks ====</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>==== DB_remarks ====</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>Missing DB remarks data can be found here <del class="diffchange diffchange-inline">missing eggNOG data can be found here: </del>ftp://ftp.sanger.ac.uk/pub2/wormbase/releases/WS229/patches/misc_DB_remark.ace</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>Missing DB remarks data can be found here ftp://ftp.sanger.ac.uk/pub2/wormbase/releases/WS229/patches/misc_DB_remark.ace</div></td></tr>
</table>
Matuli
https://wiki.wormbase.org/index.php?title=WS229&diff=12975&oldid=prev
Matuli at 16:05, 8 December 2011
2011-12-08T16:05:18Z
<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<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 16:05, 8 December 2011</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;">__TOC__</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;"></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;">=== Release Notes ===</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;"></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 WS229</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 WS229</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l478" >Line 478:</td>
<td colspan="2" class="diff-lineno">Line 482:</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>____________ 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 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><pre></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><<ins class="diffchange diffchange-inline">/</ins>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> </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 class="diffchange diffchange-inline">=== Bug Fixes ===</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 class="diffchange diffchange-inline">==== DB_remarks ====</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 class="diffchange diffchange-inline">Missing DB remarks data can be found here missing eggNOG data can be found here: ftp://ftp.sanger.ac.uk/pub2/wormbase/releases/WS229/patches/misc_DB_remark.ace</ins></div></td></tr>
</table>
Matuli
https://wiki.wormbase.org/index.php?title=WS229&diff=12898&oldid=prev
Mh6: make it readable
2011-12-06T16:52:47Z
<p>make it readable</p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<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 16:52, 6 December 2011</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 WS229</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 WS229</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-l477" >Line 477:</td>
<td colspan="2" class="diff-lineno">Line 478:</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>____________ 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;"><pre></ins></div></td></tr>
</table>
Mh6
https://wiki.wormbase.org/index.php?title=WS229&diff=12813&oldid=prev
Matuli: Created page with 'New release of WormBase WS229 WS229 was built by Mary Ann Tuli ================================ The WS229 build directory includes: species/ DIR - contains a sub …'
2011-11-25T13:36:06Z
<p>Created page with 'New release of WormBase WS229 WS229 was built by Mary Ann Tuli ================================ The WS229 build directory includes: species/ DIR - contains a sub …'</p>
<p><b>New page</b></p><div>New release of WormBase WS229<br />
<br />
WS229 was built by Mary Ann Tuli<br />
================================<br />
<br />
The WS229 build directory includes:<br />
species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:<br />
- G_SPECIES.WS229.genomic.fa.gz - Unmasked genomic DNA<br />
- G_SPECIES.WS229.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA<br />
- G_SPECIES.WS229.genomic_softmasked.fa.gz - Soft-masked (repeats lower-cased) genomic DNA<br />
- G_SPECIES.WS229.protein.fa.gz - Current live protein set<br />
- G_SPECIES.WS229.cds_transcripts.fa.gz - Spliced cDNA sequence for the CDS portion of protein-coding transcripts<br />
- G_SPECIES.WS229.ncrna_transcripts.fa.gz - Spliced cDNA sequence for non-coding RNA transcripts<br />
- G_SPECIES.WS229.intergenic_sequences.fa.gz - DNA sequence between pairs of adjacent genes<br />
- G_SPECIES.WS229.annotations.gff[2|3].gz - Sequence features in either GFF2 or GFF3 format<br />
- G_SPECIES.WS229.ests.fa.gz - ESTs and mRNA sequences extracted from the public databases<br />
- G_SPECIES.WS229.best_blastp_hits.txt.gz - Best blastp matches to human, fly, yeast, and non-WormBase Uniprot proteains<br />
- G_SPECIES.WS229.*pep_package.tar.gz - latest version of the [worm|brig|bren|rema|jap|ppa]pep package (if updated since last release)<br />
- annotation/ - contains additional annotations:<br />
- G_SPECIES.WS229.confirmed_genes.txt.gz - DNA sequences of all genes confirmed by EST &/or cDNA<br />
- G_SPECIES.WS229.cDNA2orf.txt.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)<br />
- G_SPECIES.WS229.geneIDs.txtgz - list of all current gene identifiers with CGC & molecular names (when known)<br />
- G_SPECIES.WS229.PCR_product2gene.txt.gz - Mappings between PCR products and overlapping Genes<br />
- G_SPECIES.WS229.*oligo_mapping.txt.gz - Oligo array mapping files<br />
- G_SPECIES.WS229.knockout_consortium_alleles.xml.gz - Table of Knockout Consortium alleles<br />
- G_SPECIES.WS229.SRA_gene_expression.tar.gz - Tables of gene expression values computed from SRA RNASeq data<br />
acedb DIR - Everything needed to generate a local copy of the The Primary database<br />
- database.WS229.*.tar.gz - compressed acedb database for new release<br />
- models.wrm.WS229 - the latest database schema (also in above database files)<br />
- WS229-WS228.dbcomp - log file reporting difference from last release<br />
- *Non_C_elegans_BLASTX/ - This directory contains the blastx data for non-elegans species<br />
(reduces the size of the main database)<br />
COMPARATIVE_ANALYSIS DIR - comparative analysis files<br />
- compara.WS229.tar.bz2 - gene-tree and alignment GFF files<br />
- wormpep_clw.WS229.sql.bz2 - ClustalW protein multiple alignments<br />
ONTOLOGY DIR - gene_associations, obo files for (phenotype GO anatomy) and associated association files<br />
<br />
<br />
Release notes on the web:<br />
-------------------------<br />
http://www.wormbase.org/wiki/index.php/Release_Schedule<br />
<br />
<br />
C. elegans Synchronisation with GenBank / EMBL:<br />
-----------------------------------------------<br />
<br />
No synchronisation issues<br />
<br />
<br />
C. elegans Chromosomal Changes:<br />
-------------------------------<br />
There are no changes to the chromosome sequences in this release.<br />
<br />
<br />
C. elegans Gene data set (Live C. elegans genes 47512)<br />
------------------------------------------------------<br />
Molecular_info 45859 (96.5%)<br />
Concise_description 5901 (12.4%)<br />
Reference 14295 (30.1%)<br />
WormBase_approved_Gene_name 26474 (55.7%)<br />
RNAi_result 24684 (52%)<br />
Microarray_results 23986 (50.5%)<br />
SAGE_transcript 19199 (40.4%)<br />
<br />
<br />
C. elegans <br />
<br />
Wormpep data set:<br />
-----------------<br />
<br />
There are 25547 CDSs, from 20514 protein-coding genes<br />
<br />
The 25547 sequences contain base pairs in total.<br />
<br />
Modified entries 115<br />
Deleted entries 78<br />
New entries 234<br />
Reappeared entries 6<br />
<br />
Net change +162<br />
<br />
C. elegans Genome sequence composition:<br />
---------------------------------------<br />
<br />
WS229 WS228 change<br />
----------------------------------------------<br />
a 32367418 32367418 +0<br />
c 17780787 17780787 +0<br />
g 17756985 17756985 +0<br />
t 32367086 32367086 +0<br />
n 0 0 +0<br />
- 0 0 +0<br />
<br />
Total 100272276 100272276 +0<br />
<br />
<br />
Pristionchus pacificus Genome sequence composition:<br />
----------------------------<br />
172773083 total<br />
a 43813958<br />
c 32811034<br />
g 32828589<br />
t 43810996<br />
- 0<br />
n 19508506<br />
<br />
<br />
Caenorhabditis remanei Genome sequence composition:<br />
----------------------------<br />
145500347 total<br />
a 42927857<br />
c 26293828<br />
g 26276020<br />
t 42923178<br />
- 0<br />
n 7079464<br />
<br />
<br />
Caenorhabditis japonica Genome sequence composition:<br />
----------------------------<br />
166565019 total<br />
a 46865690<br />
c 30244493<br />
g 30234317<br />
t 46807519<br />
- 0<br />
n 12413000<br />
<br />
<br />
Caenorhabditis briggsae Genome sequence composition:<br />
----------------------------<br />
108419768 total<br />
a 32984239<br />
c 19684682<br />
g 19693545<br />
t 33054090<br />
- 0<br />
n 3003212<br />
<br />
<br />
Caenorhabditis brenneri Genome sequence composition:<br />
----------------------------<br />
190421492 total<br />
a 52222485<br />
c 32837458<br />
g 32882838<br />
t 52164077<br />
- 0<br />
n 20314634<br />
<br />
<br />
<br />
<br />
Tier II Gene counts<br />
---------------------------------------------<br />
pristionchus Gene count 24216 (Coding 24216)<br />
remanei Gene count 32431 (Coding 31471)<br />
japonica Gene count 29962 (Coding 29962)<br />
briggsae Gene count 23048 (Coding 21962)<br />
brenneri Gene count 32257 (Coding 30667)<br />
---------------------------------------------<br />
<br />
<br />
<br />
<br />
-------------------------------------------------<br />
Pristionchus pacificus Protein Stats:<br />
-------------------------------------------------<br />
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)<br />
-------------------------------------------------<br />
Confirmed 229 (0.9%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 4982 (20.6%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 19006 (78.5%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Pristionchus pacificus entries with WormBase-approved Gene name 3202<br />
<br />
<br />
<br />
<br />
-------------------------------------------------<br />
Caenorhabditis remanei Protein Stats:<br />
-------------------------------------------------<br />
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)<br />
-------------------------------------------------<br />
Confirmed 956 (3.0%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 5662 (18.0%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 24858 (79.0%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Caenorhabditis remanei entries with WormBase-approved Gene name 5741<br />
<br />
<br />
<br />
<br />
-------------------------------------------------<br />
Caenorhabditis japonica Protein Stats:<br />
-------------------------------------------------<br />
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)<br />
-------------------------------------------------<br />
Confirmed 176 (0.5%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 578 (1.6%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 35351 (97.9%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Caenorhabditis japonica entries with WormBase-approved Gene name 4735<br />
<br />
<br />
<br />
<br />
-------------------------------------------------<br />
Caenorhabditis briggsae Protein Stats:<br />
-------------------------------------------------<br />
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)<br />
-------------------------------------------------<br />
Confirmed 53 (0.2%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 853 (3.9%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 21080 (95.9%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Status of entries: Protein Accessions<br />
-------------------------------------<br />
UniProtKB accessions 21682 (98.6%)<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Caenorhabditis briggsae entries with WormBase-approved Gene name 5801<br />
<br />
<br />
<br />
<br />
-------------------------------------------------<br />
Caenorhabditis brenneri Protein Stats:<br />
-------------------------------------------------<br />
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)<br />
-------------------------------------------------<br />
Confirmed 1510 (4.9%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 5638 (18.4%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 23522 (76.7%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Caenorhabditis brenneri entries with WormBase-approved Gene name 3303<br />
<br />
<br />
<br />
<br />
-------------------------------------------------<br />
Caenorhabditis elegans Protein Stats:<br />
-------------------------------------------------<br />
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)<br />
-------------------------------------------------<br />
Confirmed 12227 (47.9%) Every base of every exon has transcription evidence (mRNA, EST etc.)<br />
Partially_confirmed 11272 (44.1%) Some, but not all exon bases are covered by transcript evidence<br />
Predicted 2048 (8.0%) No transcriptional evidence at all<br />
<br />
<br />
<br />
Status of entries: Protein Accessions<br />
-------------------------------------<br />
UniProtKB accessions 24534 (96.0%)<br />
<br />
Status of entries: Protein_ID's in EMBL<br />
---------------------------------------<br />
Protein_id 25296 (99.0%)<br />
<br />
Gene <-> CDS,Transcript,Pseudogene connections<br />
----------------------------------------------<br />
Caenorhabditis elegans entries with WormBase-approved Gene name 24866<br />
<br />
<br />
C. elegans Operons Stats<br />
---------------------------------------------<br />
Description: These exist as closely spaced gene clusters similar to bacterial operons<br />
---------------------------------------------<br />
| Live Operons 1390 |<br />
| Genes in Operons 3634 |<br />
---------------------------------------------<br />
<br />
<br />
GO Annotation Stats WS229<br />
--------------------------------------<br />
<br />
GO_codes - used for assigning evidence<br />
--------------------------------------<br />
IC Inferred by Curator<br />
IDA Inferred from Direct Assay<br />
IEA Inferred from Electronic Annotation<br />
IEP Inferred from Expression Pattern<br />
IGI Inferred from Genetic Interaction<br />
IMP Inferred from Mutant Phenotype<br />
IPI Inferred from Physical Interaction<br />
ISS Inferred from Sequence (or Structural) Similarity<br />
NAS Non-traceable Author Statement<br />
ND No Biological Data available<br />
RCA Inferred from Reviewed Computational Analysis<br />
TAS Traceable Author Statement<br />
------------------------------------------------<br />
<br />
Total number of Gene::GO connections: 294649<br />
<br />
Genes Stats:<br />
----------------<br />
Genes with GO_term connections 95546 <br />
IEA GO_code present 89484 <br />
non-IEA GO_code present 6058 <br />
<br />
Source of the mapping data <br />
Source: *RNAi (GFF mapping overlaps) 25751 <br />
*citace 2456 <br />
*Inherited (motif & phenotype) 15080 <br />
<br />
GO_terms Stats:<br />
---------------<br />
Total No. GO_terms 30571 <br />
GO_terms connected to Genes 3438 <br />
GO annotations connected with IEA 1786 <br />
GO annotations connected with non-IEA 1640 <br />
Breakdown IC - 4 IDA - 445 ISS - 150 <br />
IEP - 11 IGI - 137 IMP - 792 <br />
IPI - 79 NAS - 2 ND - 1 <br />
RCA - 0 TAS - 18 <br />
<br />
<br />
-===================================================================================-<br />
<br />
Useful Stats:<br />
---------<br />
<br />
Genes with Sequence and WormBase-approved Gene names<br />
WS229 47648 (24866 elegans / 5801 briggsae / 5741 remanei / 4735 japonica / 3303 brenneri / 3202 pristionchus)<br />
<br />
<br />
-===================================================================================-<br />
<br />
<br />
<br />
New Data:<br />
---------<br />
1) DNAse1 sites<br />
<br />
7095 Features marking DNAse1 hypersensitive sites have been added to the database.<br />
These have a Method of "DNAseI_hypersensitive_site".<br />
<br />
They are from the paper:<br />
Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites<br />
Shi B, Guo X, Wu T, Sheng S, Wang J, Skogerbo G, Zhu X, Chen R<br />
BMC Genomics 2009, 10:92<br />
doi:10.1186/1471-2164-10-92 PMID 19243610<br />
<br />
http://www.biomedcentral.com/1471-2164/10/92<br />
<br />
The hypersensitive sites found fall into three categories: those cut only by 240 U/ml, only by 480 U/ml and those cut by both.<br />
<br />
2) Ascaris suum<br />
<br />
A draft genome including a preliminary gene set, based on "Ascaris<br />
suum draft genome",Rex et.al,doi:10.1038/nature10553 has been added.<br />
<br />
GFF3 and fasta files of the protein set and genome can be<br />
downloaded from ftp.wormbase.org in addition to accessing it through<br />
GBrowse and blast server. Ortholog C.elegans genes are also<br />
annotated.<br />
<br />
3) Heterorhabditis bactieriophora:<br />
<br />
A H.bacteriophora genome based on a draft assembly from WashU St.Louis<br />
has been added and is available as fasta and GFF3 for download and<br />
viewable on GBrowse and blast. A gene set is expected from the<br />
H.bacteriphora curation group for a future release.<br />
<br />
4) Bursephelenchus xylophilus<br />
<br />
A draft genome of B.xylophilus based on "Genomic Insights into the<br />
Origin of Parasitism in the Emerging Plant Pathogen Bursephelenchus<br />
xylophilus", Kikuchi et al., doi:10.1371/journal.ppat.1002219 has been<br />
added.<br />
<br />
It also includes a gene set provided by the authors<br />
and is available as fasta and GFF3 file for download from ftp.wormbase.org in addition <br />
to accessing it through GBrowse and blast.<br />
<br />
<br />
Other Changes:<br />
--------------<br />
1) Genome Sequence error sites<br />
<br />
A set of errors in the reference sequence have been identified by comparison of the N2 genome to the sister strain LSJ2 (which diverged from <br />
N2 before N2 was split up into lab specific strains):<br />
<br />
Nature. 2011 Aug 17;477(7364):321-5. doi: 10.1038/nature10378.<br />
Parallel evolution of domesticated Caenorhabditis species targets pheromone receptor genes.<br />
McGrath PT, Xu Y, Ailion M, Garrison JL, Butcher RA, Bargmann CI.<br />
<br />
This has resulted in 882 Features with the Method "Genome_sequence_error" being made to mark the positions of the insertion or deletion errors.<br />
The reference sequence has not yet been changed as a consequence because changes to the reference sequence make difficulties for people who <br />
require a stable genome sequence coordinate system.<br />
<br />
There are 39 CDS models that will be changed as a consequence of these sequence errors and there are 15 Pseudogenes that will be <br />
re-examined because of these errors.<br />
<br />
2) GI numbers have been updated to use the Nov 2011 GI protein IDs.<br />
<br />
<br />
Model Changes:<br />
------------------------------------<br />
Additions:<br />
<br />
1) ?Strain - new tags: <br />
Sample_history Text<br />
Date_first_frozen UNIQUE DateType<br />
<br />
<br />
2) ?Gene/?CDS/?Pseudogene/?Transcript - new tag:<br />
<br />
RNASeq_FPKM ?Life_stage Float #Evidence<br />
<br />
Notes: FPKM is the cufflinks measure of RNASeq transcript abundance - "Fragments Per Kilobase of exon per Million fragments mapped". <br />
Is like RPKM, but makes a correction for when using paired-reads.<br />
<br />
<br />
<br />
Modifications:<br />
<br />
3) ?Sequence <br />
<br />
Checksum MD5 Text //checksums should only be created for an upper-cased sequence.<br />
CRC64 Text //checksums should only be created for an upper-cased sequence.<br />
<br />
becomes:<br />
<br />
Checksum MD5 UNIQUE Text //checksums should only be created for an upper-cased sequence.<br />
CRC64 UNIQUE Text //checksums should only be created for an upper-cased sequence.<br />
<br />
4) ?Transcript - Cosmetic change to allow ACeDB code to dump the data stored in this tag correctly. <br />
<br />
Brief_identification UNIQUE Text // [020306 kj]<br />
<br />
becomes:<br />
<br />
Brief_identification UNIQUE ?Text<br />
<br />
<br />
For more info mail worm@sanger.ac.uk<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>
Matuli