Nontuberculous mycobacteria (NTM) are a large, diverse group of ubiquitous environmental organisms found in tap water, soil, dust, plants, animals, and food. NTM infection can cause various diseases, such as pulmonary disease (PD), which are most frequently observed in immunocompromised individuals. Diseases associated with NTM are particularly severe in those receiving tumor necrosis factor (T...

environment is to modulate binding interactions between proteins and glycoconjugates [6, 7]. In contrast to the large number of sulfotransferases eukaryotic systems into the domain of Prokarya. Rhizo-bia are nitrogen-fixing bacteria that enter into a symbi-Berkeley, California 94720 otic relationship with a variety of legumes. The sulfotran-sferases, NodH and NoeE, catalyze the sulfation of sec...

MOTIVATION Alternative splicing is central for cellular processes and substantially increases transcriptome and proteome diversity. Aberrant splicing events often have pathological consequences and are associated with various diseases and cancer types. The emergence of next-generation RNA sequencing (RNA-seq) provides an exciting new technology to analyse alternative splicing on a large scale. ...

UNLABELLED Multiple sequence alignment (MSA) is a central tool in most modern biology studies. However, despite generations of valuable tools, human experts are still able to improve automatically generated MSAs. In an effort to automatically identify the most reliable MSA for a given protein family, we propose a very simple protocol, named AQUA for 'Automated quality improvement for multiple s...

MOTIVATION Simple bioinformatic tools are frequently used to analyse time-series datasets regardless of their ability to deal with transient phenomena, limiting the meaningful information that may be extracted from them. This situation requires the development and exploitation of tailor-made, easy-to-use and flexible tools designed specifically for the analysis of time-series datasets. RESULT...

UNLABELLED A software package, IndexToolkit, aimed at overcoming the disadvantage of FASTA-format databases for frequent searching, is developed to utilize an indexing strategy to substantially accelerate sequence queries. IndexToolkit includes user-friendly tools and an Application Programming Interface (API) to facilitate indexing, storage and retrieval of protein sequence databases. As open ...

Context. IC 10 X-1 has recently been confirmed as a black hole (BH) + Wolf-Rayet (WR) X-ray binary, and NGC 300 X-1 is thought to be. The only other known BH+WR candidate is Cygnus X-3. IC 10 X-1 and NGC 300 X-1 have similar X-ray properties, with 0.3–10 keV luminosities ∼1038 erg s−1, and their X-ray lightcurves exhibit orbital periods ∼30 h. Aims. We investigate similarities between IC 10 X-1...

Nuclear reactions occurring at densities ≈ 10 g cm in the crust of a transiently accreting neutron star efficiently maintain the core at a temperature ≈ (5–10)× 10K. When accretion halts, the envelope relaxes to a thermal equilibrium set by the flux from the hot core, as if the neutron star were newly born. For the time-averaged accretion rates (∼< 10 −10 M⊙ yr ) typical of low-mass X-ray trans...