This unit shows how to use the Bowtie package to align short sequencing reads, such as those output by second-generation sequencing instruments. It also includes protocols for building a genome index and calling consensus sequences from Bowtie alignments using SAMtools.

SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed. We adapted the compressed full-text index (BWT) used by SOAP2 in view of the advantages and disadvantages of GPU. When tested with millions of Illumina Hiseq 2000 length-100 bp reads, SOAP3 takes < 30 s to align a million read pairs onto ...

A new algorithm for removing Bowtie Effect of Moderate resolution Imaging Spectrometer (MODIS) data without utilizing the ephemeris data is proposed in this paper. Based on a thoroughly study of the observation characteristics of MODIS, and a comprehensive comparison and evaluation among the existing algorithms for removing Bowtie Effect, the new algorithm is derived with correlation coefficien...

A k-bowtie system of order v is a pair (X,B), where X is a finite set of v vertices and B is a collection of edge disjoint k-bowties (called blocks) which partitions the edge set of the complete graph Kn, defined in X. In this paper, for every admissible order v, we construct two disjoint non isomorphic 4-bowtie systems. Mathematics Subject Classification: 05B05

This article consist of two parts. In the first part, we enumerate the kite systems of order 8; in the second part, we consider embedding kite systems into bowtie systems.

BACKGROUND The four arms of the Holliday junction are known to stack in pairs forming two helical domains whose orientations are antiparallel, but twisted positively by about 60 degrees, based on electrophoretic, FRET and AFM measurements. Recent gel retardation studies suggest that a bowtie junction (containing 5',5' and 3',3' linkages in its crossover strands) may adopt a parallel conformatio...

I propose a new filtering technique to separate bathymetric data into regional and residual components. Directional median (DiM) filtering divides a given filter circle into N "bow-tie" sectors, allocates the data points inside the filter circle to each bowtie sector based on their relative position with respect to the center of the filter circle, estimates a median value for each sector, and r...

Over time, teachers collect a great deal of information about each student. Integrating that information intelligently requires models for how the students’ proficiency changes over time. Armed with such models, teachers can filter the data—more accurately estimate the student’s current proficiency levels—and forecast the student’s future proficiency level. Furthermore, partially observed Marko...

Antenna design in ultra-wideband (UWB) systems is a major challenge. For, in contrast to conventional systems, wherein waveform distortion by the antenna is negligible, there is potentially significant waveform distortion by UWB antennas. A further challenge to UWB system design is posed by mandated limits on power spectrum density, such as the FCC emission mask. In this paper, we join these tw...