Difference between revisions of "C.remanei"

From WormBaseWiki
Jump to navigationJump to search
(managed to fix it in WS188)
m
 
(5 intermediate revisions by 2 users not shown)
Line 1: Line 1:
= Overview =
+
= Overview =
== current data ==
 
The C.remanei data available in WormBase is based on the [http://genome.wustl.edu/pub/organism/Invertebrates/Caenorhabditis_remanei/assembly/Caenorhabditis_remanei-1.0/  Caenorhabditis_remanei-1.0] 6x assembly from WashU and gene predictions using the WashU merged gene prediction pipeline.  These gene predictions have not been submitted to EMBL/GenBank, but the assembly has.
 
  
== Future Data ==
+
== current data  ==
* a newer 9.2x C.remanei assembly is available from WashU [http://genome.wustl.edu/pub/organism/Invertebrates/Caenorhabditis_remanei/assembly/Caenorhabditis_remanei-15.0.1/ Caenorhabditis_remanei-15.0.1]
 
* the [[NGASP]] project plans produce a new C.remanei gene set
 
* manual curation is supposed to start as soon as [[NGASP]] predictions for the new assembly are available.
 
* EMBL/GenBank submission is supposed to start together with manual curation.
 
  
= State of Integration =
+
The C.remanei data available in WormBase is based on the [http://genome.wustl.edu/pub/organism/Invertebrates/Caenorhabditis_remanei/assembly/Caenorhabditis_remanei-1.0/ Caenorhabditis_remanei-1.0] 6x assembly from WashU and gene predictions using the WashU merged gene prediction pipeline. These gene predictions have not been submitted to EMBL/GenBank, but the assembly has.
  
As of WS188:
+
== Future Data  ==
  
== ACeDB ==
+
*a newer 9.2x C.remanei assembly is available from WashU [http://genome.wustl.edu/pub/organism/Invertebrates/Caenorhabditis_remanei/assembly/Caenorhabditis_remanei-15.0.1/ Caenorhabditis_remanei-15.0.1]
The Genes, Proteins as well as orthology predictions were imported in WS186 are are now automatically updated each build. Blast homologies to C.remanei proteins are included for C.elegans and C.briggsae proteins.
+
*the [[NGASP|NGASP]] project plans produce a new C.remanei gene set
=== known bugs ===
+
*manual curation is supposed to start as soon as [[NGASP|NGASP]] predictions for the new assembly are available.  
* The protein sequences were not imported (fixed in WS188). Protein pages and proper cross links between them and their corresponding gene pages will be available in WS189.
+
*EMBL/GenBank submission is supposed to start together with manual curation.
* some blast hits from C.elegans/C.briggsae don't link to the correct protein (fixed in WS188)
 
  
== Website ==
+
= State of Integration  =
The default code is used to show the ACeDB data and there is a GBrowse version available to show the GFF annotation. It is also included in the three-way genomic alignment viewer on the dev site.
 
=== known bugs ===
 
* the live site can't show remanei gene pages (fixed on dev)
 
* the small GBrowse window on the gene page doesn't show anything.
 
** that is due to renaming of the C.remanei contigs to resolve conflicts with C.brenneri
 
** an updated GFF file is planned for WS189 which will solve the GBrowse issues
 
  
== Flat Files ==
+
As of WS191:  
=== GFF ===
 
A GFF file including CDSes and blast hits were created for WS186 and are available at [ftp://ftp.sanger.ac.uk/pub2/wormbase/WS186/CHROMOSOMES/remagff186/ remagff186]
 
The GFF file is not yet complete and doesn't include BLAT data and Gene Spans. An updated version is planned for WS189.
 
=== Proteins ===
 
A test-version of C.remanei proteins, called remapep was done for WS186 and can be found at [ftp://ftp.sanger.ac.uk/pub2/wormbase/WS186/remapep186.gz remapep186]
 
The generation of history files and addition of all available IDs is planned for WS189.
 
=== DNA ===
 
The contigs used for annotation can be found at [ftp://ftp.sanger.ac.uk/pub2/wormbase/WS186/CHROMOSOMES/remagff186/ remagff186]. The sequences should be identically to the WashU-1.0 assembly, only contig names were prefixed with "Crem_" .
 
  
== Curation ==
+
== ACeDB  ==
* gene models will be manually curated by WashU.
 
* gene names are already curated in the traditional ex-CGC / WormGeneNames way
 
* for the current gene models only systematic errors will be fixed, as we expect NGASP to release a new geneset any day
 
  
== History ==
+
Is now fully integrated into the build.
=== 2005 ===
+
 
preliminary data was made available as flatfiles and through the WormBase GBrowse
+
 
=== WS186 ===
+
== Website  ==
integration of C.remanei data into the canonical ACeDB database
+
 
=== (future) WS189 ===
+
The default code is used to show the ACeDB data and there is a GBrowse version available to show the GFF annotation. It is also included in the three-way genomic alignment viewer on the dev site.
* integration of C.remanei into the regular build pipeline
+
 
* website fixes
+
=== known bugs  ===
=== (future) WS190 ===
+
 
* should be in a state to get included into the frozen release
+
*the small GBrowse window on the gene page doesn't show anything.
 +
 
 +
== Flat Files  ==
 +
 
 +
The files are available on the normal
 +
<pre>ftp://ftp.sanger.ac.uk/pub2/wormbase/WSxxx/genomes/remanei/</pre>
 +
replace the xxx with the release number you want.
 +
 
 +
== Curation  ==
 +
 
 +
*gene models will be manually curated by WashU.
 +
*gene names are already curated in the traditional ex-CGC / WormGeneNames way (identifiable by a Crem- prefix)
 +
*for the current gene models only systematic errors will be fixed, as we expect NGASP to release a new geneset any day
 +
 
 +
== History ==
 +
 
 +
=== 2005 ===
 +
 
 +
preliminary data was made available as flatfiles and through the WormBase GBrowse  
 +
 
 +
=== WS186 ===
 +
 
 +
integration of C.remanei data into the canonical ACeDB database  
 +
 
 +
=== WS189 ===
 +
 
 +
*integration of C.remanei into the regular build pipeline  
 +
*website fixes
 +
 
 +
=== WS190 ===
 +
 
 +
*got included into the frozen release
 +
 
 +
=== probably WS193 ===
 +
* assembly update
 +
* update of the gene-set with Jigsaw models
 +
 
 +
 
 +
[[Category:User Guide]]
 +
[[Category:Other species]]

Latest revision as of 19:34, 11 August 2010

Overview

current data

The C.remanei data available in WormBase is based on the Caenorhabditis_remanei-1.0 6x assembly from WashU and gene predictions using the WashU merged gene prediction pipeline. These gene predictions have not been submitted to EMBL/GenBank, but the assembly has.

Future Data

  • a newer 9.2x C.remanei assembly is available from WashU Caenorhabditis_remanei-15.0.1
  • the NGASP project plans produce a new C.remanei gene set
  • manual curation is supposed to start as soon as NGASP predictions for the new assembly are available.
  • EMBL/GenBank submission is supposed to start together with manual curation.

State of Integration

As of WS191:

ACeDB

Is now fully integrated into the build.


Website

The default code is used to show the ACeDB data and there is a GBrowse version available to show the GFF annotation. It is also included in the three-way genomic alignment viewer on the dev site.

known bugs

  • the small GBrowse window on the gene page doesn't show anything.

Flat Files

The files are available on the normal

ftp://ftp.sanger.ac.uk/pub2/wormbase/WSxxx/genomes/remanei/

replace the xxx with the release number you want.

Curation

  • gene models will be manually curated by WashU.
  • gene names are already curated in the traditional ex-CGC / WormGeneNames way (identifiable by a Crem- prefix)
  • for the current gene models only systematic errors will be fixed, as we expect NGASP to release a new geneset any day

History

2005

preliminary data was made available as flatfiles and through the WormBase GBrowse

WS186

integration of C.remanei data into the canonical ACeDB database

WS189

  • integration of C.remanei into the regular build pipeline
  • website fixes

WS190

  • got included into the frozen release

probably WS193

  • assembly update
  • update of the gene-set with Jigsaw models