Computer Science ›› 2017, Vol. 44 ›› Issue (10): 33-37, 50.doi: 10.11896/j.issn.1002-137X.2017.10.006

Previous Articles     Next Articles

SBV:A Bioinformatics Visualization Software Based on SVG

CAI Rui-chu, LIN Yin-xian and AI Peng   

  • Online:2018-12-01 Published:2018-12-01

Abstract: Bioinformatics visualization is an important approach to exploit the information behind the massive biological data.In view of the challenges like massive data size,accurate visualization effect and diversified visualization requirements,we presented a bioinformatics visualization software based on SVG,called SBV (SVG for Bioinformatics Visuali-zation).SBV takes advantages of scalability of SVG and customizable performance form of DOM and CSS to draw a variety of bioinformatics maps.It is a maneuverable integrative bioinformatics visualization platform supporting most of existing bioinformatics visualization requirements.The software has been open source in Github,which provides good foundation for the further development.

Key words: Bioinformatics,Visualization,SVG,Chromosome map

[1] Cline M S,Kent W J.Understanding genome browsing[J].Nature Biotechnology,2009,27(2):153-155.
[2] PAVLOPOULOS G A,IACUCCI E,ILIOPOULOS I,et al.Interpreting the Omics ‘era’ Data[M]∥Multimedia Services in Intelligent Environments.Springer International Publishing,2013:79-100.
[3] KENT W J,SUGNET C W,FUREY T S,et al.The Human Genome Browser at UCSC[J].Genome Research,2002,12(6):996.
[4] ABEEL T,VAN P T,SAEYS Y,et al.GenomeView:a next-generation genome browser[J].Nucleic Acids Research,2012,40(2):e12.
[5] ROBINSON J T,THORVALDSDTTIR H,W INCKLER W,et al.Integrative genomics viewer[J].Nature Biotechnology,2011,29(1):24-26.
[6] PEREZLLAMAS C,LOPEZBIGAS N.Gitools:Analysis andVisualisation of Genomic Data Using Interactive Heat-Maps[J].Plos One,2011,6(6):e19541.
[7] SEVERIN J,LIZIO M,HARSHBARGER J,et al.Interactivevisualization and analysis of large-scale sequencing datasets using ZENBU[J].Nature Biotechnology,2014,32(3):217-219.
[8] MEDINA I,SALAVERT F,SANCHEZ R,et al.GenomeMaps,a new generation genome browser[J].Nucleic Acids Research,2013,41(Web Server issue):41-46.
[9] SHANNON P,MARKIEL A,OZIER O,et al.Cytoscape:A software environment for integrated models of biomolecular interaction networks[J].Genome Res,2003,13:2498-2504.
[10] KRZYWINSKI M,SCHEIN J,BIROL ,et al.Circos:An information aesthetic for comparative genomics[J].Genome Res,2009,19:1639-1645.
[11] WHEELER D L,CHURCH D M,F EDERHEN S,et al.Database resources of the national center for biotechnology[J].Nucleic Acids Research,2003,31(1):28-33.
[12] WESTESSON O,SKINNER M,HOLMES I.Visualizing next-generation sequencing data with JBrowse[J].Briefings in Bioinformatics,2013,14(2):172-177.
[13] MUKHYALA K,MASSELOT A.Visualization of protein se-quence features using JavaScript and SVG with pViz.js[J].Bioinformatics,2014,30(23):3408-3409.
[14] PAVLOPOULOS G A,MALLIARAKIS D, PAPANIKOLAOU N,et al.Visualizing genome and systems biology:technologies,tools,implementation techniques and trends,past,present and future[J].GigaScience,2015,4(1):38.

No related articles found!
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
[1] LEI Li-hui and WANG Jing. Parallelization of LTL Model Checking Based on Possibility Measure[J]. Computer Science, 2018, 45(4): 71 -75, 88 .
[2] XIA Qing-xun and ZHUANG Yi. Remote Attestation Mechanism Based on Locality Principle[J]. Computer Science, 2018, 45(4): 148 -151, 162 .
[3] LI Bai-shen, LI Ling-zhi, SUN Yong and ZHU Yan-qin. Intranet Defense Algorithm Based on Pseudo Boosting Decision Tree[J]. Computer Science, 2018, 45(4): 157 -162 .
[4] WANG Huan, ZHANG Yun-feng and ZHANG Yan. Rapid Decision Method for Repairing Sequence Based on CFDs[J]. Computer Science, 2018, 45(3): 311 -316 .
[5] SUN Qi, JIN Yan, HE Kun and XU Ling-xuan. Hybrid Evolutionary Algorithm for Solving Mixed Capacitated General Routing Problem[J]. Computer Science, 2018, 45(4): 76 -82 .
[6] ZHANG Jia-nan and XIAO Ming-yu. Approximation Algorithm for Weighted Mixed Domination Problem[J]. Computer Science, 2018, 45(4): 83 -88 .
[7] WU Jian-hui, HUANG Zhong-xiang, LI Wu, WU Jian-hui, PENG Xin and ZHANG Sheng. Robustness Optimization of Sequence Decision in Urban Road Construction[J]. Computer Science, 2018, 45(4): 89 -93 .
[8] LIU Qin. Study on Data Quality Based on Constraint in Computer Forensics[J]. Computer Science, 2018, 45(4): 169 -172 .
[9] ZHONG Fei and YANG Bin. License Plate Detection Based on Principal Component Analysis Network[J]. Computer Science, 2018, 45(3): 268 -273 .
[10] SHI Wen-jun, WU Ji-gang and LUO Yu-chun. Fast and Efficient Scheduling Algorithms for Mobile Cloud Offloading[J]. Computer Science, 2018, 45(4): 94 -99, 116 .