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