1,816 research outputs found
Detecting Superbubbles in Assembly Graphs
We introduce a new concept of a subgraph class called a superbubble for
analyzing assembly graphs, and propose an efficient algorithm for detecting it.
Most assembly algorithms utilize assembly graphs like the de Bruijn graph or
the overlap graph constructed from reads. From these graphs, many assembly
algorithms first detect simple local graph structures (motifs), such as tips
and bubbles, mainly to find sequencing errors. These motifs are easy to detect,
but they are sometimes too simple to deal with more complex errors. The
superbubble is an extension of the bubble, which is also important for
analyzing assembly graphs. Though superbubbles are much more complex than
ordinary bubbles, we show that they can be efficiently enumerated. We propose
an average-case linear time algorithm (i.e., O(n+m) for a graph with n vertices
and m edges) for graphs with a reasonable model, though the worst-case time
complexity of our algorithm is quadratic (i.e., O(n(n+m))). Moreover, the
algorithm is practically very fast: Our experiments show that our algorithm
runs in reasonable time with a single CPU core even against a very large graph
of a whole human genome.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
The first determination of the actinide Th abundance for a red giant of the Ursa Minor dwarf galaxy
The Thorium abundance for the red giant COS82 in the Ursa Minor dwarf
spheroidal galaxy is determined based on a high resolution spectrum. This is
the first detection of actinides in an extra Galactic object. A detailed
abundance pattern is determined for 12 other neutron-capture elements from the
atomic number 39 to 68. These elements are significantly over-abundant with
respect to other metals like Fe (> 1 dex) and their abundance pattern agrees
well with those of the r-process-enhanced, very metal-poor stars known in the
Galactic halo, while the metallicity of this object ([Fe/H] ~ -1.5) is much
higher than these field stars ([Fe/H] ~ -3.0). The results indicate that the
mechanism and the astrophysical site that are responsible for neutron-capture
elements in COS82 is similar to that for field r-process-enhanced stars, while
the condition of low mass star formation is quite different. An estimate of the
age of this object based on the Th abundance ratio is discussed.Comment: 5 pages, 2 figures, 1 table, to appear in PAS
From Theory to Practice: Plug and Play with Succinct Data Structures
Engineering efficient implementations of compact and succinct structures is a
time-consuming and challenging task, since there is no standard library of
easy-to- use, highly optimized, and composable components. One consequence is
that measuring the practical impact of new theoretical proposals is a difficult
task, since older base- line implementations may not rely on the same basic
components, and reimplementing from scratch can be very time-consuming. In this
paper we present a framework for experimentation with succinct data structures,
providing a large set of configurable components, together with tests,
benchmarks, and tools to analyze resource requirements. We demonstrate the
functionality of the framework by recomposing succinct solutions for document
retrieval.Comment: 10 pages, 4 figures, 3 table
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