Visualization Tools
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This document discusses several visualization tools used for genomics research including: - Ensembl, which produces genome databases for vertebrates and eukaryotes. - JalView, a program for multiple sequence alignment editing, visualization and analysis. - G-Compass, a comparative genome browser that visualizes conserved regions between human and 12 other vertebrates. - JBrowse, a speedy genome browser with a responsive interface for visualizing genome data. - Tablet, a lightweight viewer for next-generation sequencing assemblies and alignments.
Visualization Tools
- 3. Ensembl produces genome databases for vertebrates and other eukaryotic species
- 5. JalView JalView 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.
- 7. 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
- 8. JBrowse Speedy genome browser with a responsive and dynamic Ajax interface for visualization of genome data
- 9. JBrowse
- 10. Tablet A lightweight, high-performance graphical viewer for ngs assemblies and alignments
- 11. Tablet
- 12. 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.
- 13. 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).
Editor's Notes
- #3: Purpose of the Visualization step is that it enables bioinformaticians to interpret information obtained from RNA seq data, allow users to browse mapped experimental data with different types of annotation, and also allows comparison of multiple organisms or individuals
- #4: http://www.molbiol.ox.ac.uk/courses/Ensembl.shtml http://www.ensembl.org/index.html Ensembl allows scientist the ability to access the human genome and other organism such as mouse and chimpanzee. With Ensembl researches can perform searches on chromosomal DNA.
- #5: As you can see in this diagram, the Human CDNA is being compared to the Mouse cDNA
- #6: http://www.jalview.org/node/187 http://www.virology.ws/2010/10/20/viral-bioinformatics-multiple-sequence-alignment-jalview/
- #7: http://bioinformatics.oxfordjournals.org/content/25/24/3321.full http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089445
- #8: http://h-invitational.jp/g-compass/
- #9: http://jbrowse.org/ http://seqanswers.com/wiki/JBrowse
- #10: http://jbrowse.org/ Provides a fast, smooth analysis of genome Scales easily to multi-gigabase genomes and deep-coverage sequencing Support many output formats (e.g. BED, FASTA, BAM, etc.) Requires very little server resources Huge datasets from a single low-cost cloud instance
- #11: http://www.molecularevolution.org/software/genomics/tablet
- #12: http://bioinformatics.oxfordjournals.org/content/26/3/401/F1.expansion.html http://compfly.bio.ub.es/CONSOLIDERcourse2011June/05_Day5/04_geneannotation/web/gassembly.html Features a high-performance visualization and data navigation Display of reads in packed and/or stacked formats Entire-contig overviews, showing data layout or coverage information
- #13: 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).