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. 2015 Oct 15;31(20):3359-61.
doi: 10.1093/bioinformatics/btv362. Epub 2015 Jun 10.

IBS: an illustrator for the presentation and visualization of biological sequences

Wenzhong Liu  1 , Yubin Xie  2 , Jiyong Ma  2 , Xiaotong Luo  2 , Peng Nie  2 , Zhixiang Zuo  3 , Urs Lahrmann  4 , Qi Zhao  2 , Yueyuan Zheng  2 , Yong Zhao  2 , Yu Xue  5 , Jian Ren  6
Affiliations

IBS: an illustrator for the presentation and visualization of biological sequences

Wenzhong Liu et al. Bioinformatics. .

Abstract

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.

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Figures

Fig. 1.
Fig. 1.
The main interface of IBS. (A) The standalone software showing the domain organization of E3 SUMO-protein ligase RanBP2 (Flotho and Werner, 2012). (B) The online service presenting the organization of bromodomain proteins and translocations in cancer (Muller et al., 2011)
See this image and copyright information in PMC

References

    1. Flotho A., Werner A. (2012) The RanBP2/RanGAP1*SUMO1/Ubc9 complex: a multisubunit E3 ligase at the intersection of sumoylation and the RanGTPase cycle. Nucleus, 3, 429–432. - PMC - PubMed
    1. Muller S., et al. (2011) Bromodomains as therapeutic targets. Expert Rev. Mol. Med., 13, e29. - PMC - PubMed
    1. Ren J., et al. (2009) DOG 1.0: illustrator of protein domain structures. Cell Res., 19, 271–273. - PubMed
    1. Sigrist C.J., et al. (2013) New and continuing developments at PROSITE. Nucleic Acids Res., 41, D344–D347. - PMC - PubMed

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