The evolution of genome mining in microbes – a review
Reads0
Chats0
TLDR
Different approaches of mining genomes for secondary metabolites are focused, from detecting biosynthetic genes to resistance based methods and "evo-mining" strategies including a short evaluation of the impact of the development of genome mining methods and tools on the field of natural products and microbial ecology.About:
This article is published in Natural Product Reports.The article was published on 2016-07-27 and is currently open access. It has received 466 citations till now. The article focuses on the topics: Genome & Bacterial genome size.read more
Citations
More filters
Journal ArticleDOI
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline
Kai Blin,Simon Shaw,Katharina Steinke,Rasmus Villebro,Nadine Ziemert,Sang Yup Lee,Sang Yup Lee,Marnix H. Medema,Tilmann Weber +8 more
TL;DR: AntiSMASH 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, β-lactones, fungal RiPPs, RaS-Ri PPs, polybrominated diphenyl ethers, C-nucleosides, PPY-like ketones and lipolanthines and provides more detailed predictions for type II polyketide synthase-encoding gene clusters.
Journal ArticleDOI
Natural products in drug discovery: advances and opportunities.
TL;DR: In this article, the authors summarize recent technological developments that are enabling natural product-based drug discovery, highlight selected applications and discuss key opportunities, and discuss the potential of using natural products as drug leads.
Journal ArticleDOI
antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.
Kai Blin,Thomas Wolf,Marc G. Chevrette,Xiaowen Lu,Christopher J. Schwalen,Satria A. Kautsar,Hernando G. Suarez Duran,Emmanuel L. C. de los Santos,Hyun Uk Kim,Mariana Nave,Jeroen S. Dickschat,Douglas A. Mitchell,Ekaterina Shelest,Rainer Breitling,Eriko Takano,Sang Yup Lee,Tilmann Weber,Marnix H. Medema +17 more
TL;DR: The thoroughly updated antiSMASH version 4 is presented, 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, and several usability features have been updated and improved.
Journal ArticleDOI
antiSMASH 6.0: improving cluster detection and comparison capabilities.
Kai Blin,Simon Shaw,Alexander M. Kloosterman,Zach Charlop-Powers,Gilles P. van Wezel,Marnix H. Medema,Marnix H. Medema,Tilmann Weber +7 more
TL;DR: antiSMASH as mentioned in this paper is the most widely used tool for detecting and characterising biosynthetic gene clusters (BGCs) in bacteria and fungi, and it is updated version 6 of antiSMASH.
Journal ArticleDOI
Nonribosomal Peptide Synthesis-Principles and Prospects.
Roderich D. Süssmuth,Andi Mainz +1 more
TL;DR: This Review provides state-of-the-art knowledge on the underlying mechanisms of NRPSs and the variety of their products along with detailed analysis of the challenges for future reprogrammed biosynthesis.
References
More filters
Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
Enzymatic assembly of DNA molecules up to several hundred kilobases
Daniel G. Gibson,Lei Young,Ray-Yuan Chuang,J. Craig Venter,Clyde A. Hutchison,Hamilton O. Smith +5 more
TL;DR: An isothermal, single-reaction method for assembling multiple overlapping DNA molecules by the concerted action of a 5′ exonuclease, a DNA polymerase and a DNA ligase is described.
Journal ArticleDOI
Fast and sensitive protein alignment using DIAMOND
TL;DR: DIAMOND is introduced, an open-source algorithm based on double indexing that is 20,000 times faster than BLASTX on short reads and has a similar degree of sensitivity.
Journal ArticleDOI
Natural Products As Sources of New Drugs over the 30 Years from 1981 to 2010
David J. Newman,Gordon M. Cragg +1 more
TL;DR: This review is an updated and expanded version of the three prior reviews and adds a new designation, "natural product botanical" or "NB", to cover those botanical "defined mixtures" that have now been recognized as drug entities by the FDA and similar organizations.
Journal ArticleDOI
HMMER web server: interactive sequence similarity searching
TL;DR: This work has focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them.
Related Papers (5)
antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.
Kai Blin,Thomas Wolf,Marc G. Chevrette,Xiaowen Lu,Christopher J. Schwalen,Satria A. Kautsar,Hernando G. Suarez Duran,Emmanuel L. C. de los Santos,Hyun Uk Kim,Mariana Nave,Jeroen S. Dickschat,Douglas A. Mitchell,Ekaterina Shelest,Rainer Breitling,Eriko Takano,Sang Yup Lee,Tilmann Weber,Marnix H. Medema +17 more