We are happy to announce that the Washington University Genome
Sequencing Center, St Louis
and the Sanger Institute (Cambridge) have collected approximately 10x
depth of whole genome
shotgun sequence data, and have a preliminary assembly. We are
providing BLAST servers for
the whole genome assembly at:
http://www.sanger.ac.uk/Projects/C_briggsae/blast_server.shtmlhttp://genome.wustl.edu/gsc/Blast/client.pl
This assembly has been generated using the PHUSION assembler from Jim
Mullikin (Sanger
Institute). The typical contig size is 27 kb (half the sequence is
in contigs of this
size or greater) and the typical supercontig (scaffold) size is 170
kb, so most genes
should be complete, but we are aware that there are some problems.
In particular it contains
redundancy (so the 110Mb total size of the data set is an
overestimate of the genome size),
and it does not yet incorporate the clone-based data previously
finished at the GSC.
Also, as with any automatically generated unfinished sequence it may
contain sequence
errors or missassemblies. We will be making new assemblies over the
coming weeks,
and expect to release a full sequence to the sequence databases and
by ftp once it
has stabilised.
However, despite the sequence being non-final it is very usable, and
the BLAST servers
will allow worm researchers to identify C. briggsae matches for their
sequences of
interest. We have also run the WABA program of Jim Kent (Genome
Research 10:1115-1125,
2000) to compare the entire assembly to the C. elegans genome and
have placed the results
into Wormbase, so conserved regions will be marked up at
www.wormbase.org (from version
WS60 onwards).
We hope you all find this new set of genome data useful!
The Caenorhabditis Genome Sequencing Consortium
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