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

C.remanei

Contents