(, Sigrist 2012 Feb 21;18(7):589-600. doi: 10.3748/wjg.v18.i7.589. In nucleotide mode, the transcript organization, including exon, CDS, 5-UTR, 3-UTR, and RNA modification sites (integrated from RMVar (13)), was visualized. 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. . Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user . In particular, a specially designed crystal renderer has also been developed to enhance the esthetic quality of the schematic diagrams. The installer and the software of IBS require at least a Java SE Runtime Environment(JRE) 6 to run. In 2005, Demir etal. Epub 2014 Mar 24. -. In the early 1600s, the explorer tienne de Flacourt documented his travels to Madagascar, and illustrated the unique fauna there, setting a precedent for future explorers as world travel became a more feasible reality. (. At present, biologists mainly use Microsoft PowerPoint, Adobe Illustrator or Photoshop to draw schematic diagrams for biological sequences. IBS: Illustrator for Biological Sequences In protein mode, the functional domains, repeat regions, coiled coils, motifs, and known post-translational modifications (integrated from the PTMsnp Database (12)) were automatically drawn. Copyright 2004-2023.The CUCKOO Workgroup. To allow an advanced usage of IBS, we have further developed a lightweight and speedy JavaScript library for the users. In addition, a lightweight JS library was developed in IBS 2.0 to assist the visualization of biological sequences in customized web services. Multiple op-tions are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in auser-dened mode. Here, we have developed a novel software called IBS, which is dedicated to the illustration of biological sequence organization. Ren J., Wen L., Gao X., Jin C., Xue Y., Yao X. Liu W., Xie Y., Ma J., Luo X., Nie P., Zuo Z., Lahrmann U., Zhao Q., Zheng Y., Zhao Y. et al. and transmitted securely. Multiomic analysis of cohesin reveals that ZBTB transcription factors contribute to chromatin interactions, Cas1Cas2 physically and functionally interactswith DnaK to modulate CRISPR Adaptation, Nanopore sensing reveals a preferential pathway for the co-translocational unfolding of a conjugative relaxaseDNA complex, Mechanistic insight into AP-endonuclease 1 cleavage of abasic sites at stalled replication fork mimics, Nsp14 of SARS-CoV-2 inhibits mRNA processing and nuclear export by targeting the nuclear cap-binding complex, Chemical Biology and Nucleic Acid Chemistry, Gene Regulation, Chromatin and Epigenetics, https://creativecommons.org/licenses/by-nc/4.0/, Receive exclusive offers and updates from Oxford Academic. In addition, an XML format is provided for the saving of all of the drawing details in a single project file. 2019/10/25 admin Protein Sequence Analysis Biological Sequence, IBS, Illustrator. Moreover, in consideration of the demand for the drawing of black-and-white images, IBS also provides a texture renderer. Additionally, several polyline elements were developed in nucleotide mode. As presented in previous studies (5,6), the SUMO E3 ligase RanBP2 and the Ran GTPase activating protein (RanGAP1) are known to form a stable complex during the cell cycle, which indicated a correlation between the sumoylation of proteins and RanGTP hydrolysis. Jia GS, Zhang WC, Liang Y, Liu XH, Rhind N, Pidoux A, Brysch-Herzberg M, Du LL. A concise, delicate and precise picture can afford a great advantage over description alone. The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). (B) The online service presenting the organization of bromodomain proteins and translocations in cancer (Muller etal., 2011). 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. 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. However,. An official website of the United States government. Careers. government site. IBS is a web-accessible open resource available at https://ibs.renlab.org. Published by Oxford University Press. With a dual-mode user interface, experimentalists could produce schematic diagrams of both protein and nucleotide sequences with ease. In particular, a specially designed crystal renderer has also been developed to enhance the esthetic quality of the schematic diagrams. OLeary N.A., Wright M.W., Brister J.R., Ciufo S., Haddad D., McVeigh R., Rajput B., Robbertse B., Smith-White B., Ako-Adjei D. et al. By investigating currently published papers, we collected a set of new functional elements in IBS 2.0, which allows for the use of much more abundant graphical components for representing domain organizations, epigenetic modifications, and regulatory molecules for both protein and nucleotide sequences. To gather an intact set of published biological sequence diagrams, we developed a deep learning model (Supplementary Methods and Figure S1) based on Resnet152 architecture to recognize biological sequence diagrams from published literature. Here, we present a professional tool called IBS 2.0 for illustrating the organization of both protein and nucleotide sequences. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (, 5 The color renderers for schematic diagrams, 7 The retrieval of annotations from UniProt, https://doi.org/10.1093/bioinformatics/btv362, http://creativecommons.org/licenses/by-nc/4.0/, Receive exclusive offers and updates from Oxford Academic, Autopsy Pathologist and CLIA Medical Director Leadership Opportunity University of Vermont Health Network, MEDICAL MICROBIOLOGY AND CLINICAL LABORATORY MEDICINE PHYSICIAN, CLINICAL CHEMISTRY LABORATORY MEDICINE PHYSICIAN. (C) The resource platform in IBS 2.0. However, in IBS 2.0, artwork can be saved in high-resolution bitmaps and editable vector images, which may be more suitable for producing publication-quality figures. DeepDyve's default query mode: search by keyword or DOI. At present, biologists mainly use Microsoft PowerPoint, Adobe Illustratoror Photoshop to draw schematic diagrams for biological sequences. Using the tool, the functional domains and sites of a protein sequence can be drawn to a precise scale. TBtools: An Integrative Toolkit Developed for - ScienceDirect 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. At present, biologists mainly use Microsoft PowerPoint, Adobe Illustrator or Photoshop to . At present, biologists mainly use Microsoft PowerPoint, Adobe Illustrator or Photoshop to diagram biological sequences. In the near future, we will update IBS as a comprehensive graphical software dedicated to biological research. 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. Also, when using these tools, neither the locations nor the positions of functional elements can be precisely designated in the biological sequences. et al. Run the software: In addition, in this update, a database visualization feature was also implemented for the UniProt (3) and NCBI RefSeq (4) databases. Published by Oxford University Press on behalf of Nucleic Acids Research. Job applications can be submitted to scientific researchers, publishers of scientific manuscripts, research institutions, museums, scientific foundations, commercial book publishers or university presses, individual authors, hospitals and medical training centers, local and state government offices, park services, environmental control offices, special government committees, printers and commercial publishing houses. To facilitate the drawing process, IBS is currently equipped with a database visualization feature through which users can retrieve annotations from UniProt database. Also, a variety of image formats, such as JPEG, PNG and TIFF, are supported. The site is secure. Importantly, as shown in Figure 1A, a variety of drawing elements, such as polylines, polygons and information texts, have been integrated into IBS. In addition, the backend was developed based on Java, and all data were stored and managed in MySQL. 2015 Oct 15;31(20):3359-61. doi: 10.1093/bioinformatics/btv362. Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user-defined mode. In this updated version, diagrams can be exported as an image file (in SVG, PNGor JPEG format) or a JSON file at any time. IBS 2.0: an upgraded illustrator for the visualization of biological Other functions will also be added based on suggestions and comments from our users. Thank you for submitting a comment on this article. In Figure 1B, the polygonal elements that were provided in the nucleotide mode were extensively utilized. My Biosoftware Bioinformatics Softwares Blog. (D) Visualization of the PDZ and LIM domain protein families using the batch visualization module. Using the control panel on the right side, the precise position, size, and color of the selected component can be conveniently specified and updated in real-time. Ren Lab - Publications Supplementary information: 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. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (. Require these words, in this exact order. 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. Although DOG was specifically designed for protein diagramming, a number of researchers still used it for visualizing the functional elements of nucleotide sequences. Biological illustration - Wikipedia Unauthorized use of these marks is strictly prohibited. Contact: renjian.sysu@gmail.com or xueyu@hust.edu.cn. 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. Here, we present a software packagecalled illustrator of biological sequences (IBS) that can be used for representing the organization ofeither protein or nucleotide sequences in a convenient, efcient and precise manner. 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. Benefiting from such a wealth of drawing elements, the above complex sequence structures could be visualized in a concise and clear way. IBS 2.0: an upgraded illustrator for the visualization of biological Therefore, with the help of these drawing elements, the complex genomic schematic diagram can be clearly and succinctly represented. IBS 2.0: an upgraded illustrator for the visualization of biological sequences. 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. To provide a user-friendly software package, abundant graphical elements, such as polygons, brackets, curves and polylines, are available for representing functional elements or regulatory molecules. (, Muller et al. The Medical and Biological Illustration . 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. Interestingly, although DOG was specifically designed for protein domain graphs, a number of researchers used it for visualizing the functional elements in nucleotide sequences. Particularly, a database visualization feature was also implemented in this new version. Epub 2022 Aug 27. Moreover, we implemented a database visualization module in IBS 2.0, enabling batch visualization of biological sequences from the UniProt and the NCBI RefSeq databases. 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. Received 2015 Feb 16; Revised 2015 May 14; Accepted 2015 Jun 5. All DeepDyve websites use cookies to improve your online experience. In 2009, our group also developed a software package called DOG (Ren etal., 2009) for plotting protein graphs in a step-by-step manner. To allow an advanced usage of IBS, we also developed a lightweight and speedy JavaScript library for the users. To obtain a lossless copy of the artwork, users can export the schematic diagram as a vector image in SVG format. Please check for further notifications by email. If the install package without JRE, please download from java.com . A high-quality reference genome for the fission yeast Schizosaccharomyces osmophilus. To display different modification sites or functional sites in one protein, IBS 2.0 now provides site markers with different shapes and different colors for users, as shown in Figure 2A. The complete tutorial and source code for the JavaScript library IBS.js are freely available at https://ibs.renlab.org/#/documentation. (4) The batch visualization module for the UniProt and RefSeq databases. Therefore, an interface mode with a distinct drawing style for nucleotide representation was developed. IBS: an illustrator for the presentation and visualization of It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide, This PDF is available to Subscribers Only. Select data courtesy of the U.S. National Library of Medicine. Epub 2021 Apr 20. . Employment opportunities in the biological illustration profession are fairly limited, full-time jobs are not often available, and many experienced illustrators are self-employed, on short-term contracts, or work in science communication careers with few illustration duties. FOIA IBS 2.0: an upgraded illustrator for the visualization of biological sequences Nucleic Acids Research. The scope of biological illustration can range from the whole organism level to microscopic. In addition, the cutlines were allowed to draw in the protein sequence when representing functional domains that are distant from the core regions. Download: 2023 Feb 17;24(4):4078. doi: 10.3390/ijms24044078. When using the gradient renderer to represent the functional elements or annotations, the color and the direction can be discretionarily varied by users. In the mid-16th century, the physician Andreas Vesalius compiled and published the De humani corporis fabrica, a collection of textbooks on human anatomy superior to any illustrations that had been produced until that point. 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. To display different functional sites in one protein, IBS also provides site markers with different shapes and colors for users, as demonstrated in Figure 1A. . In this work, we present a new tool called illustrator of biological sequences (IBS) for assisting biologists in drawing publication-quality diagrams of both protein and nucleotide sequences. Please read the FAQs of User Guide. Federal government websites often end in .gov or .mil. By means of the export module, a publication-quality figure could be generated. Ren J., Wen L., Gao X., Jin C., Xue Y., Yao X.. DOG 1.0: illustrator of protein domain structures. it allows applications to export their graphics into SVGPDF and EPS format. However, these software packages were developed to meet the general needs of image manipulation, and the locations of functional elements cannot be precisely designated in the biological sequences. Bethesda, MD 20894, Web Policies 2022 Nov;106:154419. doi: 10.1016/j.phymed.2022.154419. 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. For example, the scale of functional elements such as DNA motifs and protein domains is typically approximated, even judged by eye. Digital illustration can be done using a monitor or drawing tablet, computer software such as Adobe Illustrator or Photoshop, or it can be used in post-production after the illustration has been drawn by hand. Therefore, with the help of such powerful drawing elements, the complex genomic schematic diagram can be clearly and succinctly represented. In addition to the earlier features, we also developed several professional color renderers in IBS. However, due to the limitations of the currently used applications, there are still considerable challenges in the preparation of biological schematic diagrams. The frontend of IBS 2.0 was built using HTML5, CSS, JavaScriptand the library SVG.js (https://svgjs.dev/docs/3.0/) for manipulating and animating biological sequences. Careers, Unable to load your collection due to an error. The first attempt at providing a professional illustrator of MyDomains for biological sequences was made by the PROSITE database (Sigrist et al., 2013).
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