Difference between revisions of "C.remanei"
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− | = Overview = | + | = Overview = |
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− | == | + | == current data == |
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− | + | 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 == | |
− | + | *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|NGASP]] project plans produce a new C.remanei gene set | |
− | + | *manual curation is supposed to start as soon as [[NGASP|NGASP]] predictions for the new assembly are available. | |
− | * | + | *EMBL/GenBank submission is supposed to start together with manual curation. |
− | * | ||
− | == | + | = State of Integration = |
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− | + | As of WS191: | |
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− | == | + | == ACeDB == |
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− | == 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 | + | |
− | === | + | 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 === |
− | === | + | |
− | * | + | *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
Contents
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