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 | |||
• 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 | |
• 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 |