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. 2022 Jul 5;50(W1):W420-W426.
doi: 10.1093/nar/gkac373.

IBS 2.0: an upgraded illustrator for the visualization of biological sequences

Yubin Xie  1 , Huiqin Li  1 , Xiaotong Luo  2 , Hongyu Li  1 , Qiuyuan Gao  1 , Luowanyue Zhang  1 , Yuyan Teng  1 , Qi Zhao  2 , Zhixiang Zuo  2 , Jian Ren  1   2
Affiliations

IBS 2.0: an upgraded illustrator for the visualization of biological sequences

Yubin Xie et al. Nucleic Acids Res. .

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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Figures

Graphical Abstract
Graphical Abstract
IBS 2.0: an upgraded illustrator for the visualization of biological sequences.
Figure 1.
Figure 1.
Overview of the IBS 2.0 server. (A) The main interface of IBS consists of 5 functional parts. (1) The component list panel showing the functional elements drawn in the presented sequence diagram. (2) A toolbox that contains buttons for generating various functional elements in the biological sequences. Some operation commands, such as New, Import, Export, Undo, Redo, Center, Zoom, etc., were also implemented in the toolbox. (3) The interactive interface for drawing biological sequence diagrams. (4) The batch visualization module for the UniProt and RefSeq databases. (5) The interface for setting properties of the selected element. (B) The main pipeline constructed for the batch visualization module. (C) The resource platform in IBS 2.0. Existing biological sequence diagrams can be uploaded, retrieved, and browsed via this module.
Figure 2.
Figure 2.
Schematic representation of two selected biological sequences. (A) A schematic diagram of the E3 SUMO-protein ligase RanBP2. A RanGAP1-induced activation process is presented on the domain graph. (B) Organization of the fru gene in Drosophila melanogaster. Sex-specific alternative splicing is shown.
Figure 3.
Figure 3.
A snapshot of the batch visualization module in IBS 2.0. (A) The data input panel. (B) Retrieval results from the UniProt (left) and RefSeq (right) databases. (C) The main interface of the resource platform. (D) Visualization of the PDZ and LIM domain protein families using the batch visualization module. (E) Visualization of the TGFB1 transcript isoforms using the batch visualization module.
See this image and copyright information in PMC

References

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