Geneious Basic
Matthew Kearse,Richard Moir,Amy Wilson,Steven Stones-Havas,Matthew Cheung,Shane Sturrock,Simon Buxton,Alex Cooper,Sidney Markowitz,Chris Duran,Tobias Thierer,Bruce Ashton,Peter Meintjes,Alexei J. Drummond +13 more
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TLDR
Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types.Abstract:
Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data.
Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.
Contact: peter@biomatters.comread more
Citations
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Journal ArticleDOI
High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects
Benjamin P. Kleinstiver,Vikram Pattanayak,Michelle S. Prew,Shengdar Q. Tsai,Nhu T. Nguyen,Zongli Zheng,J. Keith Joung +6 more
TL;DR: With its exceptional precision, SpCas9-HF1 provides an alternative to wild-type Sp Cas9 for research and therapeutic applications and suggests a general strategy for optimizing genome-wide specificities of other CRISPR-RNA-guided nucleases.
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Rationally Engineered Cas9 Nucleases With Improved Specificity
TL;DR: In this paper, the authors used structure-guided protein engineering to improve the specificity of Streptococcus pyogenes Cas9 (SpCas9) using targeted deep sequencing and unbiased whole-genome off-target analysis to assess Cas9-mediated DNA cleavage in human cells.
Journal ArticleDOI
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
Tilmann Weber,Kai Blin,Srikanth Duddela,Daniel Krug,Hyun Uk Kim,Robert E. Bruccoleri,Sang Yup Lee,Sang Yup Lee,Michael A. Fischbach,Rolf Müller,Wolfgang Wohlleben,Rainer Breitling,Eriko Takano,Marnix H. Medema,Marnix H. Medema +14 more
TL;DR: AntiSMASH as mentioned in this paper is a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.org.
Journal ArticleDOI
PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies
TL;DR: PhyloSuite is designed for both beginners and experienced researchers, allowing the former to quick‐start their way into phylogenetic analysis, and the latter to conduct, store and manage their work in a streamlined way, and spend more time investigating scientific questions instead of wasting it on transferring files from one software program to another.
Journal ArticleDOI
Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts.
Todd C. LaJeunesse,John Everett Parkinson,Paul W. Gabrielson,Hae Jin Jeong,James Davis Reimer,Christian R. Voolstra,Scott R. Santos +6 more
TL;DR: It is proposed that evolutionarily divergent Symbiodinium "clades" are equivalent to genera in the family Symbiodiniaceae, and formal descriptions for seven of them are provided, and the date for the earliest diversification of this family to the middle of the Mesozoic Era is amended.
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