The Rsamtools package provides an interface to BAM files. BAM files are produced by samtools and other software, and represent a flexible format for storing ‘short’ reads aligned to reference genomes. BAM files typically contain sequence and base qualities, and alignment coordinates and quality measures. BAM files are appealing for several reasons. The format is flexible enough to represent rea...

The development of new antibiotics is particularly problematic in Gram-negative bacteria due to the presence outer membrane (OM), which serves as a permeability barrier. Recently, β-barrel assembly machine (BAM), located OM and responsible for type protein (OMP) assembly, has been validated novel target antibiotics. Here, we identified potential BAM complex inhibitors using screening approach t...

In this paper,the exponential passivity criteria for BAM neural networks with time-varying delays is studied.By constructing new Lyapunov-Krasovskii functional and dividing the delay interval into multiple segments,a novel sufficient condition is established to guarantee the exponential stability of the considered system.Finally,a numerical example is provided to illustrate the usefulness of th...

MOTIVATION The reference CRAM file format implementation is in Java. We present 'Scramble': a new C implementation of SAM, BAM and CRAM file I/O. RESULTS The C implementation of for CRAM is 1.5-1.7× slower than BAM at decoding but 1.8-2.6× faster at encoding. We see file size savings of 34-55%. AVAILABILITY AND IMPLEMENTATION Source code is available at http://sourceforge.net/projects/stade...

2,6-Dichlorobenzamide (BAM), a persistent metabolite from the herbicide 2,6-dichlorobenzonitrile (dichlobenil), is the pesticide residue most frequently detected in Danish groundwater. A BAM-mineralizing bacterial community was enriched from dichlobenil-treated soil sampled from the courtyard of a former plant nursery. A BAM-mineralizing bacterium (designated strain MSH1) was cultivated and ide...

BAM (2,6-dichlorobenzamide) is a metabolite of the pesticide dichlobenil. Naturally occurring bacteria that can utilize BAM are rare. Often the compound cannot be degraded before it reaches the groundwater and therefore it poses a serious threat to drinking water supplies. The bacterial strain Aminobacter MSH1 is a BAM degrader and therefore a potential candidate to be amended to sand filters i...