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Table 4 Genome browsers

From: Unraveling genomic variation from next generation sequencing data

Tool Purpose Properties Support Availability
AnnoJ [97] Deep sequencing and other genome annotation data Implemented by users, to handle data and render it into a visible form. Web 2.0 application implemented in JavaScript Web 2.0 javascript application
Plugin architecture
Smooth navigation
Distribution of work between the server and the client with distant access through web services
Argo Manual annotations of complete genomes ComBo comparative viewer to view dot plots of multiple aligned sequences FASTA, Genbank, GFF, BLAST, BED, Wiggle and Genscan files Stand-alone java application that can be launched as an applet or a java web start
CGView [98] Static and interactive graphical maps of circular genomes using a circular layout Export of graphical maps in PNG, JPG or SVG formats Series of hyperlinked maps showing expanded views Implemented in Java and it comes with its own API
XML formats
Generation of a series of hyperlinked maps showing expanded views
Combo [99] Dynamic browser to visualize alignments of whole genomes and their associated annotations Use of a dot plot view Zoom in and out at various resolutions Stand-alone java application
Highlighted views of detailed information from specific alignments and annotations Its own file format
Ensembl [100, 101] Annotation, analysis and display of various genomes Optimized to serve thousands users per day and handling large amounts of data API for accessing and associating genome-scale data from different species across the taxonomy Web application
GBrowse [102, 103] Combination of databases and interactive web pages to manipulate and display genome annotations GBrowse_syn is an extension to show dot-plots for comparative genomics “rubber band” interface to allow faster zooming Component of the Generic Model Organism System Database Project (GMOD) [104]
HTML/Javascript
Genome Projector [105] Circular genome maps, traditional genome maps, plasmid maps, biochemical pathways maps and DNA walks Limited to bacterial species with circular chromosomes Google Maps API to offer smoother navigation and better searching functionality Web application
It comes with its own API
IGB [106] Optimized to achieve maximum flexibility and high quality genome visualization Visualization of tiling array data, NGS results, genome annotations, microarray designs and the sequence itself Rapid navigation through multiple zooming scales and across large regions of genomic sequence Stand-alone java application
Ability to handle huge datasets and diverse data sources and formats
IGV [107] High-performance and ability to interactively explore and integrate large datasets Sequence alignments, microarrays, and genomic annotations Great variety of input file formats Standalone application
Integration of meta-data as heatmaps for deeper analysis
UCSC Cancer Genomics Browser [108] Integration of clinical data Heatmaps Searching capabilities to find patterns in the huge amounts of clinical and genomic data that are gathered in large-scale cancer studies Web application
Boxplots
Proportions
UCSC Genome Browser [109] Rapid linear visualization, examination, and querying of the data at many levels and it currently accommodates genomes of ~50 species • Gene Sorter: expression, homology and other information among related groups of genes. Annotation datasets: mRNA alignments, mappings of DNA repeat elements, gene predictions, gene-expression data, disease-association data Genome Graphs for uploading and displaying genome-wide data sets
• Blat: mapping any sequence to the genome while the Table Browser provides direct access to the underlying database.
• VisiGene: browsing through a large collection of in situ mouse and frog images to examine expression patterns
Panning, zooming, and dragging capabilities increase the quality of interaction
Uploading a large variety of files
User specific customized sessions.
X:map [110] Mappings between genomic features and Affymetrix microarrays Location of individual exon probes with respect to their target genes, transcripts and exons. Google Maps API to analyse and further visualize data through an associated BioConductor package Web application