Visualization of protein sequence features using Java']JavaScript and SVG with pViz.js']js

被引:13
作者
Mukhyala, Kiran [1 ]
Masselot, Alexandre [1 ]
机构
[1] Genentech Inc, Dept Bioinformat & Computat Biol, San Francisco, CA 94080 USA
关键词
D O I
10.1093/bioinformatics/btu567
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
pViz.js is a visualization library for displaying sequence features in a Web browser. By simply providing a and the locations of its features, this lightweight, yet JavaScript library renders an interactive view of the protein Interactive exploration of protein sequence features over the Web is common need in Bioinformatics. Although many Web sites developed viewers to display these features, their are usually focused on data from a specific source or use Some of these viewers can be adapted to fit other use cases are not designed to be reusable. pViz makes it easy to display as boxes aligned to a protein sequence with zooming functionality also includes predefined renderings for secondary structure and translational modifications. The library is designed to further this view. We demonstrate such applications of pViz using examples: a proteomic data visualization tool with an viewer for displaying features on protein structure, and a tool to alize the results of the variant_effect_predictor tool from Ensembl.
引用
收藏
页码:3408 / 3409
页数:2
相关论文
共 10 条
[1]  
[Anonymous], NUCL ACID RES
[2]  
Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkh121, 10.1093/nar/gkr1065]
[3]   The Protein Data Bank [J].
Berman, HM ;
Westbrook, J ;
Feng, Z ;
Gilliland, G ;
Bhat, TN ;
Weissig, H ;
Shindyalov, IN ;
Bourne, PE .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242
[4]   The Distributed Annotation System [J].
Dowell, Robin D. ;
Jokerst, Rodney M. ;
Day, Allen ;
Eddy, Sean R. ;
Stein, Lincoln .
BMC BIOINFORMATICS, 2001, 2 (1)
[5]   BioJS']JS: an open source Java']JavaScript framework for biological data visualization [J].
Gomez, John ;
Garcia, Leyla J. ;
Salazar, Gustavo A. ;
Villaveces, Jose ;
Gore, Swanand ;
Garcia, Alexander ;
Martin, Maria J. ;
Launay, Guillaume ;
Alcantara, Rafael ;
del-Toro, Noemi ;
Dumousseau, Marine ;
Orchard, Sandra ;
Velankar, Sameer ;
Hermjakob, Henning ;
Zong, Chenggong ;
Ping, Peipei ;
Corpas, Manuel ;
Jimenez, Rafael C. .
BIOINFORMATICS, 2013, 29 (08) :1103-1104
[6]   neXtProt: a knowledge platform for human proteins [J].
Lane, Lydie ;
Argoud-Puy, Ghislaine ;
Britan, Aurore ;
Cusin, Isabelle ;
Duek, Paula D. ;
Evalet, Olivier ;
Gateau, Alain ;
Gaudet, Pascale ;
Gleizes, Anne ;
Masselot, Alexandre ;
Zwahlen, Catherine ;
Bairoch, Amos .
NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D76-D83
[7]   UniProt Knowledgebase: a hub of integrated protein data [J].
Magrane, Michele .
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2011,
[8]   Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor [J].
McLaren, William ;
Pritchard, Bethan ;
Rios, Daniel ;
Chen, Yuan ;
Flicek, Paul ;
Cunningham, Fiona .
BIOINFORMATICS, 2010, 26 (16) :2069-2070
[9]   Protter: interactive protein feature visualization and integration with experimental proteomic data [J].
Omasits, Ulrich ;
Ahrens, Christian H. ;
Mueller, Sebastian ;
Wollscheid, Bernd .
BIOINFORMATICS, 2014, 30 (06) :884-886
[10]   Jalview Version 2-a multiple sequence alignment editor and analysis workbench [J].
Waterhouse, Andrew M. ;
Procter, James B. ;
Martin, David M. A. ;
Clamp, Michele ;
Barton, Geoffrey J. .
BIOINFORMATICS, 2009, 25 (09) :1189-1191