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

Liu W, Xie Y, Ma J, Luo X, Nie P, Zuo Z, Lahrmann U, Zhao Q, Zheng Y, Zhao Y, Xue Y, Ren J - Bioinformatics (2015)

Bottom Line: 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.Also, the final representational artwork can be directly exported into a publication-quality figure.The standalone package of IBS was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China, Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073, China.

No MeSH data available.


Related in: MedlinePlus

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)
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btv362-F1: 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)

Mentions: Using options such as multiple sequence presentation, the polygonal elements for sequence annotation and enhanced markers for presenting functional sites, the protein DOG can be generated in a convenient manner. When drawing under the protein mode, the protein sequences, as well as their functional domains and sites, can be precisely pinpointed by simply specifying the starting and ending positions. Importantly, as shown in Figure 1A, a variety of drawing elements, such as polylines, polygons and information texts, have been integrated into IBS. As a result of such a wealth of drawing elements, the interaction factors as well as their annotation notes of a given protein can be easily marked on the biological sequences, which will be a great help in interpreting novel regulatory models. 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. 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.Fig. 1.


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

Liu W, Xie Y, Ma J, Luo X, Nie P, Zuo Z, Lahrmann U, Zhao Q, Zheng Y, Zhao Y, Xue Y, Ren J - Bioinformatics (2015)

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)
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4595897&req=5

btv362-F1: 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)
Mentions: Using options such as multiple sequence presentation, the polygonal elements for sequence annotation and enhanced markers for presenting functional sites, the protein DOG can be generated in a convenient manner. When drawing under the protein mode, the protein sequences, as well as their functional domains and sites, can be precisely pinpointed by simply specifying the starting and ending positions. Importantly, as shown in Figure 1A, a variety of drawing elements, such as polylines, polygons and information texts, have been integrated into IBS. As a result of such a wealth of drawing elements, the interaction factors as well as their annotation notes of a given protein can be easily marked on the biological sequences, which will be a great help in interpreting novel regulatory models. 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. 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.Fig. 1.

Bottom Line: 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.Also, the final representational artwork can be directly exported into a publication-quality figure.The standalone package of IBS was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China, Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073, China.

No MeSH data available.


Related in: MedlinePlus