freely available for academic research. Contact: renjian.sysu@gmail.com or xueyu@hust.edu.cn. Please enable it to take advantage of the complete set of features! et al. . Nevertheless, similar to MyDomains, only one protein was allowed to draw in these kinds of websites at a time. First, MyDomains only supports drawing protein diagrams with up to 6 different shapes and 4 colors, while IBS 2.0 provides 22 types of graphical elements and any desired color for producing both protein and nucleotide sequence diagrams. If this is indeed the intention of the illustration, it would be the world's first anatomical illustration.[3]. IBS provides a dual-mode interface to effectively assist the illustrative diagram for either protein or nucleotide sequences. Also, we have provided three color renderers for a better color appearance. The installer and the software of IBS require at least a Java SE Runtime Environment(JRE) 6 to run. have any concerns. -, Liu W., Xie Y., Ma J., Luo X., Nie P., Zuo Z., Lahrmann U., Zhao Q., Zheng Y., Zhao, UniProt C. UniProt: the universal protein knowledgebase in 2021. Taken together, we propose that IBS 2.0 could be a great help for molecular and cellular experimentalists, allowing them to present the nucleotide organization in a more efficient, aesthetic, and concise manner. 2009).Also, the scales and positions of functional domains and sites can be precisely defined by users. Up to six different shapes and four different color modes are supported in the diagramming of the protein domains. Unable to load your collection due to an error, Unable to load your delegates due to an error, Schematic representation of two selected biological sequences. Transcripts from the P2P4 promoters are not sex-specifically spliced and encode a set of common Fru isoforms that control the development of both sexes. With the abundant graphical elements provided in IBS 2.0, biological sequences can be easily represented in a concise and clear way. To obtain the latest version of IBS 2.0, please visit https://ibs.renlab.org. The site is secure. Bioinformatics The Medical and Biological Illustration . They were placed on your computer when you launched this website. For this purpose, a new software package has been introduced called ILLUSTRATOR Of BIOLOGICAL SEQUENCE (IBS) which is used for representing the organization of protein or nucleotide sequences in an easy, efficient and precise manner. Moreover, in consideration of the demand for the drawing of black-and-white images, IBS also provides a texture renderer. In addition to the earlier features, we also developed several professional color renderers in IBS. Types of biological illustrations include: Historically, biological illustrations have been in use since the beginning of man's exploration and attempts to understand the world around him. Here, we present a software package called illustrator of biological sequences (IBS) that can be used for representing the organization of . Within the dual mode, a variety of drawing elements are implemented for the annotations of both protein and nucleotide sequences. Multiple op-tions are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in auser-dened mode. 2015 Jun 10. pii: btv362. Here, we have developed a novel software called IBS, which is dedicated to the illustration of biological sequence organization. The latest version of IBS software is available from http://ibs.biocuckoo.org Copyright (c) 2007-2015. IBS Manual Illustrator for Biological Sequences Version 1.0 07/11/2015 Author: Jian Ren & Yu Xue Contact: Dr. Jian Ren, renjian.sysu@gmail.com ; Dr. Yu Xue, xueyu@hust.edu.cn The software is only free for academic research. When you try to install the software in Mac OS, but the installer says the file is damaged and can't be opened. BioSequences provides data types and methods for common operations with biological sequences, including DNA, RNA, and amino acid sequences. Additionally, to allow sharing diagrams between different tools, standard interchange formats, such as the Systems Biology Graphical Notation (17), will be further supported in our feature version. Abundant graphical elements are available for representing functional elements or regulatory molecules for both protein and nucleotide sequences. National Library of Medicine G3 (Bethesda). As a major update in the protein mode, a variety of drawing elements, such as polylines, polygons, and information texts, were integrated into IBS 2.0. The color and thickness of the polylines can be varied to represent more diversified content in functional genes. IBS is a software package that can be used for representing the organization of either protein or nucleotide sequences, in a convenient, efficient and precise manner. To provide a drawing environment without restriction, abundant graphical elements, such as polygons, brackets, curves, and polylines, were available. In particular, a specially designed crystal renderer has also been developed to enhance the esthetic quality of the schematic diagrams. A RanGAP1-induced activation process is presented on the domain graph. Ren J., Wen L., Gao X., Jin C., Xue Y., Yao X.. DOG 1.0: illustrator of protein domain structures. LeNovere N., Hucka M., Mi H., Moodie S., Schreiber F., Sorokin A., Demir E., Wegner K., Aladjem M.I., Wimalaratne S.M. The standalone packages of IBS were implemented in JAVA, and supported three major Operating Systems, including Windows, Linux and Mac OS. Yan B, Chang C, Gu Y, Zheng N, Fang Y, Zhang M, Wang G, Zhang L. Int J Mol Sci. The color and thickness of the polylines can be varied to represent more diversified content in functional genes. (A) The main interface of IBS consists of 5 functional parts. Furthermore, to increase the design efficiency, a resource platform that allows uploading, retrieval, and browsing of existing biological sequence diagrams has been integrated into IBS 2.0. Second, MyDomains can only plot one protein each time, but IBS 2.0 is free to add sequences without this restriction. Current Accreditation: 2019-2026 . Oxford University Press is a department of the University of Oxford. The JSON file records the detailed information of each functional element in the input biological sequences. For full access to this pdf, sign in to an existing account, or purchase an annual subscription. installation. The authors wish it to be known that, in their opinion, the first three authors should be regarded as Joint First Authors. With a dual-mode user interface, experimentalists are allowed to produce their own schematic diagrams for either protein or nucleotide sequences in a convenient manner. The first attempt at providing a professional illustrator of MyDomains for biological sequences was made by the PROSITE database (Sigrist et al., 2013). the contents by NLM or the National Institutes of Health. IBS: an illustrator for the presentation and visualization of biological sequences. 2012 Feb 21;18(7):589-600. doi: 10.3748/wjg.v18.i7.589. Using this JS library, users can easily visualize a biological sequence diagram in their customized web services and make it possible to present functional annotations dynamically during analysis or predictions. Recently, several similar tools have been developed for the visualization of biological sequences. To allow an advanced usage of IBS, we have further developed a lightweight and speedy JavaScript library for the users. During his five-year voyage aboard HMSBeagle, Charles Darwin wrote and illustrated The Voyage of the Beagle, which was published in 1839. ( A ), MeSH Many illustrators prefer the flexibility of their own working arrangements, but this is only possible when they are well established in the field and capable of locating work when needed. Potential of natural products in the treatment of irritable bowel syndrome. In addition, the cut- and dashed lines allow the protein sequence to be drawn when representing the functional domains that are distant from the core regions. IBS 2.0: an upgraded illustrator for the visualization of biological sequences Nucleic Acids Research. In males, the S exon is spliced at its default male-specific donor site, while a splicing event at a more 3 donor site is found in females and leads to a block translation of the following transcripts. At present, biologists mainly use MicrosoftPowerPoint,AdobeIllustratororPhotoshopto draw schematic diagrams for biological sequences. (C) The main interface of the resource platform. In our software, the gradient renderer is taken as a default style for all of the drawing elements. Notably, IBS was implemented with a configurable database visualization interface, which allows users to directly retrieve and specify annotations from UniProt database for the visualization. With a dual-mode user interface, experimentalists are allowed to produce their own schematic diagrams for either protein or nucleotide sequences in a convenient manner. Therefore, an interface mode with a distinct drawing style for nucleotide representation was developed. Existing biological sequence diagrams can be uploaded, retrieved, and browsed via this module. At present, biologists mainly use Microsoft PowerPoint, Adobe Illustrator or Photoshop to . To avoid such a scenario, we developed the cutline element to help users omit inconsequential sequences when representing functional domains that are distant from the core regions. In this resource platform, users can further edit the collected sequence diagrams using the main interface of IBS 2.0 and access the detailed information, such as the functional annotations, keywords, and associated publications, of each collected diagram. A number of new features will be added, including the drawing of organelles, metabolic pathways, and cell signaling pathways. Epub 2014 Mar 24. A user-friendly interface is provided in both the standalone package and online service of IBS. Werner 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. Up to six different shapes and four different color modes are supported in the diagramming of the protein domains. Please feel free to contact us if you A. To enhance the scalability and versatility of IBS, we have developed a lightweight and speedy JavaScript library called IBS.js that integrates all functionalities in IBS. Accessibility With the export interface, a resolution of 72, 300 and 600dpi is permitted. At present, biologists mainly use Microsoft PowerPoint, Adobe Illustrator or Photoshop to diagram biological sequences. (D) Visualization of the PDZ and LIM domain protein families using the batch visualization module. et al. Include any more information that will help us locate the issue and fix it faster for you. contact us. Unauthorized use of these marks is strictly prohibited. Overview of the IBS 2.0 server. A serine phosphorylation site at position 3207(8,9) and a lysine sumoylation site at position 2592(10) are illustrated as examples. To design sequence diagrams in IBS 2.0, users can directly drag and drop the graphical components in the main interface. DeepDyve's default query mode: search by keyword or DOI. A snapshot of the batch visualization module in IBS 2.0. Search life-sciences literature (42,393,843 articles, preprints and more) Search Please read the Manual (, Oxford University Press is a department of the University of Oxford. Therefore, with the help of such powerful drawing elements, the complex genomic schematic diagram can be clearly and succinctly represented. The visualization of biological sequences with various functional elements is fundamental for the publication of scientific achievements in the field of molecular and cellular biology. After download just double-click on the software package to begin With a dual-mode user interface, experimentalists could produce schematic diagrams of both protein and nucleotide sequences with ease. et al. The main interface of IBS. Skills development in biological illustration can involve two-dimensional art, animation, graphic design, and sculpture (such as necessary in custom prosthetics). Using this model, we collected and manually reillustrated a total of 347 diagrams in IBS 2.0. et al. Also, when using these tools, neither the locations nor the positions of functional elements can be precisely designated in the biological sequences. Published by Oxford University Press on behalf of Nucleic Acids Research. Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B. Pichler A., Knipscheer P., Saitoh H., Sixma T.K., Melchior F. Peng D., Li H., Hu B., Zhang H., Chen L., Lin S., Zuo Z., Xue Y., Ren J., Xie Y. Luo X., Li H., Liang J., Zhao Q., Xie Y., Ren J., Zuo Z. Sigrist C.J., deCastro E., Cerutti L., Cuche B.A., Hulo N., Bridge A., Bougueleret L., Xenarios I. Mistry J., Chuguransky S., Williams L., Qureshi M., Salazar G.A., Sonnhammer E.L.L., Tosatto S.C.E., Paladin L., Raj S., Richardson L.J. The graphical representation of biological sequences with various functional elements is fundamental for the efficient introduction and interpretation of scientific findings obtained in the course of the investigation of molecular biological functions. The authors wish it to be known that, in their opinion, the first three authors should be regarded as Joint First Authors. At present, biologists mainly use Microsoft PowerPoint, Adobe Illustrator or Photoshop to diagram biological sequences. Then follow the user prompts through the installation. Furthermore, to increase the design efficiency, a resource platform that allows uploading, retrieval, and browsing of existing biological sequence diagrams has been integrated into IBS 2.0. With the export interface, a resolution of 72, 300 and 600dpi is permitted. At present, biologists mainly use Microsoft PowerPoint, Adobe Illustrator or Photoshop to draw schematic diagrams for biological sequences. To provide a convenient means for preparing publication-quality figures, we have developed a fully functional export module for schematic diagrams. Meanwhile, a batch mode was also provided for the visualization of multiple protein or gene entries. Liu W, Xie Y, Ma J, Luo X, Nie P, Zuo Z, Lahrmann U, Zhao Q, Zheng Y, Zhao Y, Xue Y, Ren J. Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user-defined mode. Other functions will also be added based on suggestions and comments from our users. Sex-specific alternative splicing is shown. In 2009, our group also developed a software package called DOG (Ren etal., 2009) for plotting protein graphs in a step-by-step manner. Please Search for other works by this author on: *To whom correspondence should be addressed. Careers, Unable to load your collection due to an error. When using the gradient renderer to represent the functional elements or annotations, the color and the direction can be discretionarily varied by users. Moreover, in consideration of the demand for the drawing of black-and-white images, IBS also provides a texture renderer. For instance, the previous versions were not smooth enough to perform interactive operations, especially for drawing complex diagrams with a large number of elements. All the submitted diagrams will be manually reviewed for quality assurance. Using the tool, the functional domains and sites of a protein sequence can be drawn to a precise scale. In Figure 2B, the sex-specific alternative spliced transcripts are shown. The color and the thickness of the polylines can be varied to represent more diversified content in functional genes, such as different transcriptional directions or various alternative splicing events. Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user-defined mode. Careers. An official website of the United States government. The user interface of IBS 2.0 consists of three main functional modules. 17 May 2022 DOI: 10.1093/nar/gkac373 [ Abstract ] [ Full Text ] Li Chen, Tianjian Chen, Ya Zhang, Haichen Lin, Ruihan Wang, Yihang Wang, Hongyu Li, Zhixiang Zuo*, Jian Ren*, Yubin Xie*. Lab of Cell Dynamics, and Lab of Nanobiology,University of Science & Technology of China. To further facilitate the drawing process, we also implemented a batch visualization module for the automatic drawing of biological sequences retrieved from the UniProt and the NCBI RefSeq databases (Figure 1B). Run the software: Welcome to IBS! In addition, an input file in JSON format is also supported in the recent update. Using this JS library, one can easily integrate IBS into their web server and dynamically visualize their functional annotations in their analysis or predictions. Taken together, we propose that DOG 1.0 could be a great help for molecular and cellular experimentalists, allowing the presentation of protein domain structures in a more precise, convenient and . 2021 Jul 15;275:114119. doi: 10.1016/j.jep.2021.114119. In addition, the cut- and dashed lines allow the protein sequence to be drawn when representing the functional domains that are distant from the core regions. National Natural Science Foundation of China [31771462, 81772614, U1611261, 31801105, 81802438]; National Key R&D Program of China [2017YFA0106700]; Program for Guangdong Introducing Innovative and Entrepreneurial Teams [2017ZT07S096]; Guangdong Basic and Applied Basic Research Foundation [2020A1515010220]. Your comment will be reviewed and published at the journal's discretion. For ease of use of these resources, a user-friendly platform that enables users to browse and search the collected sequence diagrams was developed (Figure 3C). In addition, when drawing a long sequence of a nucleotide diagram, the functional elements within this sequence may be quite distant from each other. Moreover, unlike IBS 2.0, none of the abovementioned tools are capable of providing an interactive operation for users, therefore causing great inconveniences in the drawing process. At present, biologists mainly use Microsoft PowerPoint, Adobe Illustrator or Photoshop to draw schematic diagrams for biological sequences. An official website of the United States government. note: IBS is ONLY 2023 Apr 11;13(4):jkad028. A user-friendly interface is provided in both the standalone package and online service of IBS. In addition, to allow users to share diagrams designed on their own, an upload pipeline was also provided. (, Muller Disclaimer. sharing sensitive information, make sure youre on a federal With the help of various built-in textures, experimentalists can now illustrate black-and-white diagrams so as to be able to meet different publication requirements.
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