Beschreibung: Motivation: Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional degradation patterns. These patterns reflect the maturation processes that lead to the production of shorter RNA sequences. Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs. Results: We developed an algorithm termed SHARAKU to align two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. In contrast with previous work, SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping profiles to allow for the detection of common processing patterns. Using a benchmark simulated dataset, SHARAKU exhibited superior performance to previous methods for correctly clustering the read mapping profiles with respect to 5'-end processing and 3'-end processing from degradation patterns and in detecting similar processing patterns in deriving the shorter RNAs. Further, using experimental data of small RNA sequencing for the common marmoset brain, SHARAKU succeeded in identifying the significant clusters of read mapping profiles for similar processing patterns of small derived RNA families expressed in the brain. Availability and Implementation: The source code of our program SHARAKU is available at http://www.dna.bio.keio.ac.jp/sharaku/ , and the simulated dataset used in this work is available at the same link. Accession code: The sequence data from the whole RNA transcripts in the hippocampus of the left brain used in this work is available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession number DRA004502. Contact: yasu@bio.keio.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.

Beschreibung: We study fundamental properties of steady, spherically symmetric, isothermal galactic outflows in appropriate gravitational potential models. We aim at constructing a universal scale-free theory not only for galactic winds, but also for winds from clusters/groups of galaxies. In particular, we consider effects of mass–density distribution on the formation of transonic galactic outflows under several models of the density distribution profile predicted by cosmological simulations of structure formation based on the cold dark matter (CDM) scenario. In this study, we have clarified that there exist two types of transonic solutions: outflows from the central region and from a distant region with a finite radius, depending upon the density distribution of the system. The system with a sufficiently steep density gradient at the centre is allowed to have the transonic outflows from the centre. The resultant criterion intriguingly indicates that the density gradient at the centre must be steeper than the prediction of conventional CDM models including Navarro, Frenk & White and Moore et al. This result suggests that an additional steeper density distribution originated by baryonic systems such as the stellar component and/or the central massive black hole is required to realize transonic outflows from the central region. On the other hand, we predict the outflow, which is started at the outskirts of the galactic centre and is slowly accelerated without any drastic energy injection like starburst events. These transonic outflows may contribute secularly to the metal enrichment of the intergalactic medium.