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Abstract
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. However, due to the limitations of the currently used applications, there are still considerable challenges in the preparation of biological schematic diagrams. Here, we present a professional tool called IBS 2.0 for illustrating the organization of both protein and nucleotide sequences. With the abundant graphical elements provided in IBS 2.0, biological sequences can be easily represented in a concise and clear way. 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. 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. In addition, a lightweight JS library was developed in IBS 2.0 to assist the visualization of biological sequences in customized web services. To obtain the latest version of IBS 2.0, please visit https://ibs.renlab.org.
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Publication
IBS 2.0: an upgraded illustrator for the visualization of biological sequences
IBS 2.0: an upgraded illustrator for the visualization of biological sequencesNUCLEIC ACIDS RESEARCH. 2022
Cited by 246 articles
NLRP6 potentiates PI3K/AKT signalling by promoting autophagic degradation of p85α to drive tumorigenesis
Feng Zhi, Bowen Li, Chuanxia Zhang, Fan Xia, Rong Wang, Weihong Xie, Sihui Cai, Dawei Zhang, Ren Kong, Yiqiao Hu, Yilin Yang, Ya Peng, Jun Cui Nature Communications. 2023
Dual function of OmpM as outer membrane tether and nutrient uptake channel in diderm Firmicutes
Augustinas Silale, Yiling Zhu, Jerzy Witwinowski, Robert E. Smith, Kahlan E. Newman, Satya P. Bhamidimarri, Arnaud Baslé, Syma Khalid, Christophe Beloin, Simonetta Gribaldo, Bert van den Berg Nature Communications. 2023
Generic Diagramming Platform (GDP): a comprehensive database of high-quality biomedical graphics
Shuai Jiang, Huiqin Li, Luowanyue Zhang, Weiping Mu, Ya Zhang, Tianjian Chen, Jingxing Wu, Haoyun Tang, Shuxin Zheng, Yifei Liu, Yaxuan Wu, Xiaotong Luo, Yubin Xie, Jian Ren Nucleic Acids Research. 2024
Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across Bilateria
Kero Guynes, Luke A. Sarre, Allan M. Carrillo-Baltodano, Billie E. Davies, Lan Xu, Yan Liang, Francisco M. Martín-Zamora, Paul J. Hurd, Alex de Mendoza, José M. Martín-Durán Genome Biology. 2024
USP32 deubiquitinase: cellular functions, regulatory mechanisms, and potential as a cancer therapy target
Shuang Li, Yang Song, Kexin Wang, Guoxiang Liu, Xiaolei Dong, Fanghao Yang, Guang Chen, Can Cao, Huhu Zhang, Mengjun Wang, Ya Li, Teng Zeng, Chunyan Liu, Bing Li Cell Death Discovery. 2023
IBS: an illustrator for the presentation and visualization of biological sequences
IBS: an illustrator for the presentation and visualization of biological sequencesBIOINFORMATICS. 2015
Cited by 948 articles
Male-killing toxin in a bacterial symbiont of Drosophila
Toshiyuki Harumoto, Bruno Lemaitre Nature. 2018
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 Science. 2016
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, Régis Lemaitre, Andrei Pozniakovsky, David Drechsel, Ina Poser, Rohit V. Pappu, Simon Alberti, Anthony A. Hyman Cell. 2018
Long noncoding RNA AGPG regulates PFKFB3-mediated tumor glycolytic reprogramming
Jia Liu, Ze-Xian Liu, Qi-Nian Wu, Yun-Xin Lu, Chau-Wei Wong, Lei Miao, Yun Wang, Zixian Wang, Ying Jin, Ming-Ming He, Chao Ren, De-Shen Wang, Dong-Liang Chen, Heng-Ying Pu, Lin Feng, Bo Li, Dan Xie, Mu-Sheng Zeng, Peng Huang, Aifu Lin, Dongxin Lin, Rui-Hua Xu, Huai-Qiang Ju Nature Communications. 2020
An evolutionarily-conserved Wnt3/β-catenin/Sp5 feedback loop restricts head organizer activity in Hydra
Matthias C. Vogg, Leonardo Beccari, Laura Iglesias Ollé, Christine Rampon, Sophie Vriz, Chrystelle Perruchoud, Yvan Wenger, Brigitte Galliot Nature Communications. 2019
PMID：19153597
DOG 1.0: illustrator of protein domain structures
DOG 1.0: illustrator of protein domain structuresCELL RESEARCH. 2009
Cited by 595 articles
Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations
Trevor J. Pugh, Shyamal Dilhan Weeraratne, Tenley C. Archer, Daniel A. Pomeranz Krummel, Daniel Auclair, James Bochicchio, Mauricio O. Carneiro, Scott L. Carter, Kristian Cibulskis, Rachel L. Erlich, Heidi Greulich, Michael S. Lawrence, Niall J. Lennon, Aaron McKenna, James Meldrim, Alex H. Ramos, Michael G. Ross, Carsten Russ, Erica Shefler, Andrey Sivachenko, Brian Sogoloff, Petar Stojanov, Pablo Tamayo, Jill P. Mesirov, Vladimir Amani, Natalia Teider, Soma Sengupta, Jessica Pierre Francois, Paul A. Northcott, Michael D. Taylor, Furong Yu, Gerald R. Crabtree, Amanda G. Kautzman, Stacey B. Gabriel, Gad Getz, Natalie Jäger, David T. W. Jones, Peter Lichter, Stefan M. Pfister, Thomas M. Roberts, Matthew Meyerson, Scott L. Pomeroy, Yoon-Jae Cho Nature. 2012
Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders
Brian J. O’Roak, Laura Vives, Wenqing Fu, Jarrett D. Egertson, Ian B. Stanaway, Ian G. Phelps, Gemma Carvill, Akash Kumar, Choli Lee, Katy Ankenman, Jeff Munson, Joseph B. Hiatt, Emily H. Turner, Roie Levy, Diana R. O’Day, Niklas Krumm, Bradley P. Coe, Beth K. Martin, Elhanan Borenstein, Deborah A. Nickerson, Heather C. Mefford, Dan Doherty, Joshua M. Akey, Raphael Bernier, Evan E. Eichler, Jay Shendure Science. 2012
RAB31 marks and controls an ESCRT-independent exosome pathway
Denghui Wei, Weixiang Zhan, Ying Gao, Liyan Huang, Run Gong, Wen Wang, Ruhua Zhang, Yuanzhong Wu, Song Gao, Tiebang Kang Cell Research. 2020
The MAP4 Kinase SIK1 Ensures Robust Extracellular ROS Burst and Antibacterial Immunity in Plants
Meixiang Zhang, Yi-Hsuan Chiang, Tania Y. Toruño, DongHyuk Lee, Miaomiao Ma, Xiangxiu Liang, Neeraj K. Lal, Mark Lemos, Yi-Ju Lu, Shisong Ma, Jun Liu, Brad Day, Savithramma P. Dinesh-Kumar, Katayoon Dehesh, Daolong Dou, Jian-Min Zhou, Gitta Coaker Cell Host & Microbe. 2018
Generic Diagramming Platform (GDP): a comprehensive database of high-quality biomedical graphics
Shuai Jiang, Huiqin Li, Luowanyue Zhang, Weiping Mu, Ya Zhang, Tianjian Chen, Jingxing Wu, Haoyun Tang, Shuxin Zheng, Yifei Liu, Yaxuan Wu, Xiaotong Luo, Yubin Xie, Jian Ren Nucleic Acids Research. 2024
Documentation
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.
Function
Input
data
IBS
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data
format
()
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Language
Java
Cost
Free of charge
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Open access
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structure analysis
sequence analysis
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WEB_BROWSER
WEB_BROWSER
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