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Giant flares are poorly understood, but astronomers think they result from a sudden rearrangement of the magnetic field. One possibility is that the field high above the surface of the magnetar may become too twisted, suddenly releasing energy as it settles into a more stable configuration. Alternatively, a mechanical failure of the magnetar’s crust – a starquake – may trigger the sudden reconfiguration.
Although more specialized tools exist for the annotation of a de novo assembly (e.g., Augustus [ 17], Glimmer3 [ 18] and Prokka [ 19], which we previously wrapped for use in Galaxy [ 10, 13]), BLAST is often used for a first-pass assessment. The following example is based on a procedure that a local sequencing service, Edinburgh Genomics, had adopted as part of their quality control (later extended as described in [ 20]).Galaxy Tool Shed Repository “Filter sequences by ID”: https://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id/ While this gamma-ray burst did not cause deleterious effects for life on Earth, it has been hypothesized that a strong one originating within the Milky Way and pointed right at us could pose a danger - including mass extinctions - by subjecting Earth's surface to a flood of harmful ultraviolet radiation. The Telescope Array is uniquely positioned to detect ultra-high-energy cosmic rays. It sits at about 1,200m (4,000ft), the elevation sweet spot that allows secondary particles maximum development, but before they start to decay. Its location in Utah’s West Desert provides ideal atmospheric conditions in two ways: the dry air is crucial because humidity will absorb the ultraviolet light necessary for detection; and the region’s dark skies are essential, as light pollution will create too much noise and obscure the cosmic rays. Deepti Varshney, NCBI BLAST+ against the MAdLand (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.html Online; accessed TODAY
On Dec. 7, 2022, papers led by Rastinejad, Troja, and Mei were published in the scientific journal Nature, and a paper led by Gompertz was published in Nature Astronomy. Another popular tool for initial functional annotation of novel gene sequences is Blast2GO ( Conesa et al., 2005; Götz et al., 2008) which, in addition to its Graphical User Interface (GUI), offers a command line variant b2g4pipe (Blast2GO for pipelines) which we have wrapped for use in Galaxy. We implement whole organism scale Blast2GO in Galaxy as a simple two step pipeline, as used in Palomares-Rius et al. (2012), taking advantage of a local computing cluster:Galaxy also supports simple job splitting, which works at the datatype level, with input datatypes (such as FASTA) needing to provide a split method and output datatypes (such as tabular or BLAST XML) needing to provide a merge method. If this job splitting is enabled, BLAST searches are automatically parallelized by splitting the FASTA query file into chunks and then merging the output BLAST results. This process is done transparently to the user and enables genome-scale BLAST jobs to be spread across a cluster rather than being processed serially, providing a dramatic speedup. This article describes our NCBI BLAST+ [ 16] wrappers for Galaxy and associated tools and datatype definitions. Currently, these tools have not been made available at the public server hosted by the Galaxy Project owing to concerns over the resulting computational load (J Taylor, personal communication, 2013). However, they are available from the Galaxy Tool Shed for automated installation into a local Galaxy instance, or from our source code repository (hosted by GitHub, Inc., see Availability and requirements section), and are released under the open-source Massachusetts Institute of Technology (MIT) licence. Applications Cuccuru G, Orsini M, Pinna A, Sbardellati A, Soranzo N, Travaglione A, et al. Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics. 2014;30(13):1928–9. Future work will include additional wrappers for the remaining or new BLAST+ command line tools, exposing additional command line options via the Galaxy interface, and additional output file formats. Developments within Galaxy will also allow new functionality. For example, we hope to build on the Galaxy Visual Analysis Framework [ 40] to offer graphical representation of BLAST results within Galaxy, such as that offered by the NCBI web service. Similarly, managing local BLAST databases could be facilitated using the Data Manager Framework [ 35]. Cosmic rays, echoes of such violent celestial events, rain down on to Earth nearly constantly and can be detected by instruments, such as the Telescope Array observatory in Utah, which found the Amaterasu particle.
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