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Description: This approach
abandons the classical "overlap - layout - consensus"
approach in favor of a new Eulerian splicing graph approach
that, for the first time, resolves the problem of repeats
in fragment assembly. The splicing graph approach, in contrast
to the Celera assembler, does not mask repeats but uses them
instead as a powerful fragment assembly tool.
UCSD is interested in commercializing its rights in the fragment
assembly modules (see below). The research-quality software
modules that are available are listed below. For general information
about the EULER project see Pevzner, et al, PNAS, 98, 2001and
http://nbcr.sdsc.edu/euler/).
EULER-Compare (UCSD2002-818) consists of a Java user interface
and a C server backend. It compares different sets of contigs,
aligns them, and outputs information about the similarities
between contig sets of different DNA sequence assemblies.
The web-based Java user interface visualizes the comparison
data as a contig-comparison graph.
EULER-Connect (UCSD2002-819) is software that may be used
to find some useful reads from the discarded reads to imprve
the assembly result and expedite the sequence finishing. EULER-connect
can also verify chimeric reads
EULER-EC (UCSD2002-820) corrects errors in sequencing reads.
For each read it determines other overlapping reads and builds
a multiple alignment. Using his multiple alignment, EULER-EC
detects and corrects errors in the reads.
EULER-PCR (UCSD2002-821) designs finishing multiplex PCR
experiments for resolution of repeats that could not be resolved
by sequence assemblers due to their length. Based on the repeat
graph generated by EULER assembler (Pevzner, et al, PNAS,
98, 2001), the software identifies repeats and estimates their
multiplicities. Every individual repeat is resolved by placing
forward and reverse PCR primers at such distance from beginning
and the end of a repeat, so that all possible PCR products
have different length. Thus, deducing the correct pairing
between sequences outside of a repeat becomes a matter of
measuring PCR product length by gel electrophoresis. EULER-PCR
optimizes the number of reactions by pooling repeats that
can be resolve simultaneously in a single multiplex PCR experiment.
EULER-TR (UCSD2002-822) is software that to be used to improve
the assembly result of EULER. Based on the repeat graph generated
by the EULER assembler (Pevzner, et al. PNAS, 98, 2001), EULER-TR
can resolve tangle edges (repeat edges) by inspecting the
differences between reads fitted onto the tangled edge.
Keywords: genome assembly,
PCR, sequence finishing, EST assembly
Case Number: SD2002-818,
SD2002-819, SD2002-820, SD2002-821, SD2002-822
Inquiries To: invent@ucsd.edu
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