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antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification
Blin, Kai,Wolf, Thomas,Chevrette, Marc G.,Lu, Xiaowen,Schwalen, Christopher J.,Kautsar, Satria A.,Suarez ,Duran, Hernando G.,de ,los ,Santos, Emmanuel ,L. ,C.,Kim, Hyun Uk,Nave, Ma Oxford University Press 2017 Nucleic acids research Vol.45 No.w1
<P><B>Abstract</B></P><P>Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the ‘antibiotics and secondary metabolite analysis shell—antiSMASH’ has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of <I>trans</I>-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules.</P>
Bianco, F. B.,Zhang, Z.-W.,Lehner, M. J.,Mondal, S.,King, S.-K.,Giammarco, J.,Holman, M. J.,Coehlo, N. ,K.,Wang, J.-H.,Alcock, C.,Axelrod, T.,Byun, Y.-I.,Chen, W. P.,Cook, K. H.,Dave, R.,de Pater, American Institute of Physics 2010 The Astronomical journal Vol.139 No.4
<P>We have analyzed the first 3.75 years of data from the Taiwanese American Occultation Survey (TAOS). TAOS monitors bright stars to search for occultations by Kuiper Belt objects (KBOs). This data set comprises 5 × 10<SUP>5</SUP> star hours of multi-telescope photometric data taken at 4 or 5 Hz. No events consistent with KBO occultations were found in this data set. We compute the number of events expected for the Kuiper Belt formation and evolution models of Pan & Sari, Kenyon & Bromley, Benavidez & Campo Bagatin, and Fraser. A comparison with the upper limits we derive from our data constrains the parameter space of these models. This is the first detailed comparison of models of the KBO size distribution with data from an occultation survey. Our results suggest that the KBO population is composed of objects with low internal strength and that planetary migration played a role in the shaping of the size distribution.</P>
UPPER LIMITS ON THE NUMBER OF SMALL BODIES IN SEDNA-LIKE ORBITS BY THE TAOS PROJECT
Wang, J.-H.,Lehner, M. J.,Zhang, Z.-W.,Bianco, F. B.,Alcock, C.,Chen, W.-P.,Axelrod, T.,Byun, Y.-I.,Coehlo, N. ,K.,Cook, K. H.,Dave, R.,de Pater, I.,Porrata, R.,Kim, D.-W.,King, S.-K.,Lee, T.,Lin, American Institute of Physics 2009 The Astronomical journal Vol.138 No.6
<P>We present the results of a search for occultation events by objects at distances between 100 and 1000 AU in light curves from the Taiwanese-American Occultation Survey. We searched for consecutive, shallow flux reductions in the stellar light curves obtained by our survey between 2005 February 7 and 2006 December 31 with a total of ~4.5 × 10<SUP>9</SUP> three-telescope simultaneous photometric measurements. No events were detected, allowing us to set upper limits on the number density as a function of size and distance of objects in Sedna-like orbits, using simple models.</P>