As the CLC Assembly Cell software is proprietary, our exemplar workflow, available from the Galaxy Tool Shed [ 22] and myExperiment [ 23], starts from a previously generated or imported transcriptome assembly. This workflow analyses a sample of 1000 sequences only and uses Galaxy data manipulation tools to produce a sorted tally table of species hits suitable for visualization within Galaxy as a pie chart. If required, rather than extracting complete contigs, Galaxy has tools for working with genomic intervals that could be used to select the matched regions only, as in the next example. Identifying candidate gene clusters Giant flares from magnetars in the Milky Way and its satellites evolve in a distinct way, with a rapid rise to peak brightness followed by a more gradual tail of fluctuating emission. These variations result from the magnetar’s rotation, which repeatedly brings the flare location in and out of view from Earth, much like a lighthouse.

GRBs, the most powerful explosions in the cosmos, can be detected across billions of light-years. Those lasting less than about two seconds, called short GRBs, occur when a pair of orbiting neutron stars – both the crushed remnants of exploded stars – spiral into each other and merge. Astronomers confirmed this scenario for at least some short GRBs in 2017, when a burst followed the arrival of gravitational waves – ripples in space-time – produced when neutron stars merged 130 million light-years away. The first hints of the giant explosion were spotted by Nasa’s Chandra X-ray Observatory in 2016, which showed an unusual concave edge in the Ophiuchus galaxy cluster. However, at the time the possibility of this being caused by an explosion was discounted due to the huge amount of energy required to create such a large cavity. Account icon An icon in the shape of a person's head and shoulders. It often indicates a user profile.

This may be a black hole slurping up a cloud of gas and dust

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. Plant pests and pathogens introduce effector proteins into the host plant cell (green), where they can target and manipulate plant biochemistry to the benefit of the pathogen ( Dodds & Rathjen, 2010). Effectors may be delivered by haustorial ingression from a fungus or oomycete such as P. infestans (orange), via the bacterial Type III secretion system mechanism (blue), by nematodes via injection into the plant cell though a needle-like stylet (red), or many other processes (not illustrated). Where effectors may be identified by sequence properties, candidate effector proteins can be computationally predicted using Galaxy. The original Galaxy release did not include wrappers for the standalone NCBI BLAST or BLAST+ command line tools ( Altschul et al., 1990; Camacho et al., 2009). The use of BLAST was a priority for our own work, so we developed wrappers for the core BLAST+ tools. These were initially included in the main Galaxy repository before being migrated to the Galaxy Tool Shed. The BLAST+ tools have not been made available at the http://usegalaxy.org public server due to concerns over the resulting computational load (J Taylor, pers. comm., 2013), but are pre-installed on Galaxy CloudMan images, and can easily be added to a local Galaxy installation.

Grau J, Boch J, Posch S. TALENoffer: genome-wide TALEN off-target prediction. Bioinformatics. 2013;29(22):2931–2. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23(6):673–9. However, "the probability that this happens is really negligible," said astronomer and study co-author Pietro Ubertini of the National Institute for Astrophysics in Italy. Protein BLAST database”: MadLandDB (Genome zoo) plant and algal genomes with a focus on non-seed plants and streptophyte algae (22 Dec 2022) Being much further away, around two billion light-years instead of several tens of thousands, meant that the GRB had to be exceptionally bright.Blankenberg D, Von Kuster G, Bouvier E, Baker D, Afgan E, Stoler N, et al. Dissemination of scientific software with Galaxy ToolShed. Genome Biol. 2014;15(2):403. Observing this fluctuating tail is conclusive evidence of a giant flare. Seen from millions of light-years away, though, this emission is too dim to detect with today’s instruments. Because these signatures are missing, giant flares in our galactic neighborhood may be masquerading as much more distant and powerful merger-type GRBs. Together, these tools can be used in a basic workflow that takes raw sequencing data as input, yielding a whole organism gene set that can be further analysed:

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 Shortly before 4:42 a.m. EDT on April 15, 2020, a brief, powerful burst of X-rays and gamma rays swept past Mars, triggering the Russian High Energy Neutron Detector aboard NASA’s Mars Odyssey spacecraft, which has been orbiting the Red Planet since 2001. About 6.6 minutes later, the burst triggered the Russian Konus instrument aboard NASA’s Wind satellite, which orbits a point between Earth and the Sun located about 930,000 miles (1.5 million kilometers) away. After another 4.5 seconds, the radiation passed Earth, triggering instruments on NASA’s Fermi Gamma-ray Space Telescope, as well as on the European Space Agency’s INTEGRAL satellite and Atmosphere-Space Interactions Monitor (ASIM) aboard the International Space Station. Run the blastx (or blastn) wrapper using the gene(s) of interest as the query against the new database.The effects of this gamma-ray burst were studied with the help of the China Seismo-Electromagnetic Satellite (CSES), also called Zhangheng, a Chinese-Italian mission launched in 2018. The difference between your typical gamma-ray burst and this one is about the same as the difference between the light bulb in your living room and the lit-up floodlights in a sports stadium,” says Andrew Levan, Radbound University, the Netherlands, who used the NASA/ESA/CSA James Webb Space Telescope and the NASA/ESA Hubble Space Telescope to observe the burst. 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. These events seem like they’re coming from completely different places in the sky. It’s not like there’s one mysterious source,” said Prof John Belz of the University of Utah and a co-author of the paper. “It could be defects in the structure of spacetime, colliding cosmic strings. I mean, I’m just spitballing crazy ideas that people are coming up with because there’s not a conventional explanation.” In this case, scientists think a jet would have travelled in a narrow beam for a certain distance, then hit something in space, which caused the beam to explode outwards in a burst of radio emissions. Maxim Markevitch, of Nasa’s Goddard Space Flight Center in Greenbelt, Maryland, a co-author of the paper, compared the process to a stream of air travelling down a drinking straw and then turning into a bubble at the end of the straw.

The latest observations combined data from Chandra and ESA’s XMM-Newton space observatory and radio data from the Murchison Widefield Array (MWA) in Australia and the Giant Metrewave Radio Telescope (GMRT) in India to provide compelling new evidence for the gigantic explosion. As sequencing costs have fallen, for many organisms it is now practical to sequence the entire genome when interested primarily in a single gene family. In this situation, BLAST might be used within Galaxy as follows: myExperiment Galaxy workflow for the identification of candidate genes clusters: http://www.myexperiment.org/workflows/4584.html Galaxy Tool Shed Repository “clc_assembly_cell”: https://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell/ Statistically, a GRB as bright as GRB 221009A is only expected to happen once in many thousands of years, it may even be the brightest gamma-ray burst since human civilisation began. Astronomers therefore dubbed it BOAT – the brightest of all time.

author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and}, Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752 Run “Get open reading frames (ORFs) or coding sequences (CDSs)” (or the EMBOSS tool getorf ( Rice, Longden & Bleasby, 2000) which is also available in Galaxy) to obtain a set of putative protein sequences. Compare these initial contigs to the NCBI non-redundant protein sequence database (NCBI NR) using BLASTX, requesting at most one hit and tabular output including the taxonomy fields (and optionally the hit description). Buchfink, B., C. Xie, and D. H. Huson, 2014 Fast and sensitive protein alignment using DIAMOND. Nature Methods 12: 59–60. 10.1038/nmeth.3176