C.remanei

From WormBaseWiki
Jump to: navigation, search

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