9,427 research outputs found
A comprehensive evaluation of alignment algorithms in the context of RNA-seq.
Transcriptome sequencing (RNA-Seq) overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level. The first step and a major challenge in the analysis of such experiments is the mapping of sequencing reads to a transcriptomic origin including the identification of splicing events. In recent years, a large number of such mapping algorithms have been developed, all of which have in common that they require algorithms for aligning a vast number of reads to genomic or transcriptomic sequences. Although the FM-index based aligner Bowtie has become a de facto standard within mapping pipelines, a much larger number of possible alignment algorithms have been developed also including other variants of FM-index based aligners. Accordingly, developers and users of RNA-seq mapping pipelines have the choice among a large number of available alignment algorithms. To provide guidance in the choice of alignment algorithms for these purposes, we evaluated the performance of 14 widely used alignment programs from three different algorithmic classes: algorithms using either hashing of the reference transcriptome, hashing of reads, or a compressed FM-index representation of the genome. Here, special emphasis was placed on both precision and recall and the performance for different read lengths and numbers of mismatches and indels in a read. Our results clearly showed the significant reduction in memory footprint and runtime provided by FM-index based aligners at a precision and recall comparable to the best hash table based aligners. Furthermore, the recently developed Bowtie 2 alignment algorithm shows a remarkable tolerance to both sequencing errors and indels, thus, essentially making hash-based aligners obsolete
Saffman-Taylor instability in a non-Brownian suspension: finger selection and destabilization
We study the Saffman-Taylor instability in a non-Brownian suspension by
injection of air. We find that flow structuration in the Hele-Shaw cell can be
described by an effective viscosity depending on the volume fraction. When this
viscosity is used to define the control parameter of the instability, the
classical finger selection for Newtonian fluids is recovered. However, this
picture breaks down when the cell thickness is decreased below approximatively
10 grain sizes. The discrete nature of the grains plays also a determinant role
in the the early destabilization of the fingers observed. The grains produce a
perturbation at the interface proportional to the grain size and can thus be
considered as a "controlled noise". The finite amplitude instability mechanism
proposed earlier by Bensimon et al. allows to link this perturbation to the
actual values of the destabilization threshold.Comment: 4 pages, 4 figures, submitted to PR
Boredom and Creativity in the Era of Accelerated Living
Rethinking the historical relation between boredom and creativity in the
era of accelerated living, this chapters examines the impact of neoliberal
globalisation’s culture of speed and connectivity on creative practice.
It argues that boredom today has generally shifted from being an affected aesthetic pose involving stillness and retreat to become more of
an involuntary response to the exhausting hyperactivity and excessive
production characterising contemporary life
Enhancing Dark Matter Annihilation into Neutrinos
We perform a detailed and quasi model-independent analysis of direct
annihilation of Dark Matter into neutrinos. Considering different cases for
scalar and fermionic Dark Matter, we identify several settings in which this
annihilation is enhanced, contrary to some statements in the literature. They
key point is that several restrictions of, e.g., a supersymmetric framework do
not hold in general. The mass generation mechanism of the neutrinos plays an
important role, too. We illustrate our considerations by two examples that are
not (as usually) suppressed by the smallness of the neutrino mass, for which we
also present a numerical analysis. Our results can be easily used as guidelines
for model building.Comment: 33 pages, 2 figure
Disjoint finite partial steiner triple systems can be embedded in disjoint finite steiner triple systems
AbstractThis paper shows that a pair of disjoint finite partial Steiner triple systems can be embedded in a pair of disjoint finite Steiner triple systems
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