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.
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).
Notes de l'éditeur
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
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.
As you can see in this diagram, the Human CDNA is being compared to the Mouse cDNA
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
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
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).