Visualization Tools
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Transcript of Visualization Tools
VisualizationTools Used
Visualization
Ensemblproduces genome databases for vertebrates and other eukaryotic species
JalViewJalView is a free program for multiple sequence alignment editing, visualization and analysis.
Use it to view and edit sequence alignments, analyze them with phylogenetic trees and principal components analysis (PCA) plotNExs and explore molecular structures and
annotation.
G-CompassComparative genome browser.
G-Compass
– Visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates
– 12 Vertebrates Include:• Chicken, Chimpanzee, Cow, Dog, Horse, Macaque, Medaka, Mouse, Rat, Tetraodon,
Opossum, & Zebrafish
JBrowseSpeedy genome browser with a responsive and dynamic Ajax interface for visualization of
genome data
JBrowse
TabletA lightweight, high-performance graphical viewer for ngs assemblies and alignments
Tablet
Tablet showing Illumina Solexa reads against an Arabidopsis thaliana cDNA reference sequence
(additional screenshots can be seen online at http://bioinf.scri.ac.uk/tablet/screenshots.shtml).
Milne I et al. Bioinformatics 2010;26:401-402
© The Author(s) 2009. Published by Oxford University Press.
Work Cited“Jbrowse.” SEQwiki, N.P., 6 Feb. 2013. Web. 11 Aug. 2014.
<http://seqanswers.com/wiki/JBrowse>.Kawahara, Y., R. Sukate, A. Matsuya, K. Murakami, Y. Sato, H. Zhang, T. Gojobori, To. Itoh, and T.
Imanishi. “G-compass: a we-based comparative genome browse between human and other vertebrate genomes.” Bioinformatics 25.24 (2009): 3321-3322. Print.
Lee E et al. Web Apollo: a web-based genomic annotation editing platform. Genome Biology. (2013) DOI;1Q.1186/gb-2013-14-8-r93 PMID;24000942
Skinner ME, Homes IH. Setting up the Jbrowse genome browser. Curr Protoc Bioinformatics. (2010).
Skinner, ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. Jbrowse: A next-generation genome browser.
Genome Res. (2009).