C.briggsae whole genome sequence assembly

Richard Durbin rd at sanger.ac.uk
Wed Dec 12 12:10:25 EST 2001


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.shtml
       http://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

---




More information about the Celegans mailing list