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

The discrete flavor symmetry D5

We consider the standard model (SM) extended by the flavor symmetry D5 and search for a minimal model leading to viable phenomenology. We find that it contains four Higgs fields apart from the three generations of fermions whose left- and left-handed conjugate parts do not transform in the same way under D5. We provide two numerical fits for the case of Dirac and Majorana neutrinos to show the viability of our low energy model. The fits can accommodate all data with the neutrinos being normally ordered. For Majorana neutrinos two of the right-handed neutrinos are degenerate. Concerning the Higgs sector we find that all potentials constructed with three SM-like Higgs doublets transforming as 1+2 under D5 have a further unwanted global U(1) symmetry. Therefore we consider the case of four Higgs fields forming two D5 doublets and show that this potential leads to viable solutions in general, however it does not allow spontaneous CP-violation (SCPV) for an arbitrary vacuum expectation value (VEV) configuration. Finally, we discuss extensions of our model to grand unified theories (GUTs) as well as embeddings of D5 into the continuous flavor symmetries SO(3)_f and SU(3)_f.Comment: 22 page

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