IBS: an illustrator for the presentation and visualization of biological sequences.
Wenzhong Liu,Yubin Xie,Jiyong Ma,Xiaotong Luo,Peng Nie,Zhixiang Zuo,Urs Lahrmann,Qi Zhao,Yueyuan Zheng,Yong Zhao,Yu Xue,Jian Ren +11 more
TLDR
A software package called illustrator of biological sequences (IBS) that can be used for representing the organization of either protein or nucleotide sequences in a convenient, efficient and precise manner.Abstract:
Summary: Biological sequence diagrams are fundamental for visualizing various functional elements in protein or nucleotide sequences that enable a summarization and presentation of existing information as well as means of intuitive new discoveries. Here, we present a software package called illustrator of biological sequences (IBS) that can be used for representing the organization of either protein or nucleotide sequences in a convenient, efficient and precise manner. Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user-defined mode. Also, the final representational artwork can be directly exported into a publication-quality figure. Availability and implementation: The standalone package of IBS was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available at http://ibs.biocuckoo.org. Contact: renjian.sysu@gmail.com or xueyu@hust.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.read more
Citations
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A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins
Jie Wang,Jeong-Mo Choi,Alex S. Holehouse,Hyun O. Lee,Xiaojie Zhang,Marcus Jahnel,Shovamayee Maharana,Regis P. Lemaitre,Andrei Pozniakovsky,David N. Drechsel,Ina Poser,Rohit V. Pappu,Simon Alberti,Anthony A. Hyman +13 more
TL;DR: A model is developed to show that the measured saturation concentrations of phase separation are inversely proportional to the product of the numbers of arginine and tyrosine residues, which suggests it is possible to predict phase-separation properties based on amino acid sequences.
Journal ArticleDOI
The 3.8 Å resolution cryo-EM structure of Zika virus
Devika Sirohi,Zhenguo Chen,Lei Sun,Thomas Klose,Theodore C. Pierson,Michael G. Rossmann,Richard J. Kuhn +6 more
TL;DR: The structure is mainly similar to that of other flaviviruses such as dengue virus; however, there are differences in a region that may be involved in binding to host receptors that suggests that differences in this region may influence virus transmission and disease.
Journal ArticleDOI
Glutathione S-Transferase Enzymes in Plant-Pathogen Interactions.
TL;DR: Functional studies revealed that overexpression or silencing of specific GSTs can markedly modify disease symptoms and also pathogen multiplication rates, but very limited information is available about the exact metabolic functions of disease-induced GST isoenzymes and about their endogenous substrates.
Journal ArticleDOI
Zika Virus Structure, Maturation, and Receptors.
Devika Sirohi,Richard J. Kuhn +1 more
TL;DR: Rapid progress in combining structural biology with other techniques is revealing the similarities and the differences in virion structure and function between ZIKV and related flaviviruses.
Journal ArticleDOI
The evolution and population diversity of human-specific segmental duplications
Megan Y. Dennis,Megan Y. Dennis,Lana Harshman,Bradley J. Nelson,Osnat Penn,Stuart Cantsilieris,John Huddleston,Francesca Antonacci,Kelsi Penewit,Laura Denman,Archana Raja,Carl Baker,Kenneth M. K. Mark,Maika Malig,Nicolette Janke,Claudia Yadira Espinoza,Holly A.F. Stessman,Xander Nuttle,Kendra Hoekzema,Tina A Lindsay-Graves,Richard K. Wilson,Evan E. Eichler +21 more
TL;DR: It is shown that HSDs are non-randomly organized, associate preferentially with ancestral ape duplications termed ‘core duplicons’ and evolved primarily in an interspersed inverted orientation, candidates for the evolution of human-specific adaptive traits.
References
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