Mouse Genome Resources at NCBI
The
Mouse Sequencing Consortium (MSC), an international public-private effort
to accelerate the sequencing of the mouse genome, recently announced that
it has achieved its goal to generate three-fold coverage of the mouse
DNA sequence.
Rapid
Access to Trace Data
The MSC used a whole genome shotgun sequencing approach, generating 95%
of the sequence of the mouse genome, albeit in small, unordered fragments.
The shotgun reads are available from NCBI’s Trace Archive, a novel
type of database established to make the individual raw sequence reads
publicly available. To date, the MSC has deposited more than 15 million
individual unique mouse sequence traces, searchable by BLAST.
Providing rapid access to raw data, the Trace Archive serves as a repository
for all trace data generated at the major centers involved in sequencing
efforts of various organisms. Ancillary information further describing
each of the traces is also available. In order to ensure that the public
databases remain current and comprehensive, NCBI exchanges data regularly
with the Ensembl Trace Server located at the Sanger Center. The Trace
Archive can be searched at www.ncbi.nlm.nih.gov/Traces/.
Mouse
Genome Map Viewer
The mouse genome sequencing project will next utilize larger stretches
of DNA of known map position, and assemble the fragmentary pieces of sequence
into the finished, highly accurate sequence of the mouse genome. To accommodate
this new sequence, NCBI has created a Mouse Genome Map Viewer, similar
to that used for viewing the human genome.
The map viewer currently displays a genetic linkage map, generated from
data available from the Mouse Genome Database, and a radiation hybrid
map from the Whitehead Institute and MRC-Harwell that includes genetic
loci, gene-bases STSs, and simple sequence length polymorphisms. The data
are searchable by map position, gene symbol, gene name, or marker name.
The Mouse Map Viewer can be accessed from the Genomic Biology page at
www.ncbi.nlm.nih.gov/Genomes/.
Other resources include a special BLAST form that facilitates BLAST searches
of finished mouse genome sequence (available from the Mouse Genome Sequencing
page) and a Human-Mouse Homology Map at www.ncbi.nlm.nih.gov/Homology/.
—CB, BR
