Skip to main content

Table 5 Comparative genomics

From: Unraveling genomic variation from next generation sequencing data

Tool Purpose Properties Support
Cinteny [111] Fast identification of syntenic regions Flexible parameterization Pre-loaded annotated mammalian, invertebrate and fungal genomes
User-provided data such as orthologous genes, sequence tags or other markers
ggbio [112] Views of particular genomic regions and genome-wide overviews ideograms Bioconductor Library
grand linear views
sequence fragment length
edge-linked interval to data view,
mismatch pileup,
several splicing summaries
GenomeComp [113] A tool for summarizing, parsing and visualizing a genome wide sequence comparison A tool to locate the rearrangements, insertions or deletions of genome segments between species or strains Fasta format
Genbank format
EMBL format
•BLAST output file
Circos [114] Developed to identify and analyze similarities and differences between larger genomes Circular layout It supports its own file format
Scatter, line, and histogram plots, heat maps, tiles, connectors, and text
DHPC [115] Visualization of large-scale genome sequences by mapping sequences into a two-dimensional using the space-filling function of Hilbert-Peano mapping. Repeating sequences DNA sequences can be loaded in plain text or FASTA forma
Degree of base bias
Regions of homogeneity and their boundaries,
Mark of annotated segments such as genes or isochores.
HilbertVis [116] Functions to visualize long vectors of integer data by means of Hilbert curves Chip-Seq data The stand-alone version can load GFF, BED/Wiggle and Maq map files.
Chip-chip data
Exploration at different zoom levels of detail
The R packages HilbertVis and HilbertVisGUI are integrated in the R / Bioconductor statistical environment and can display any data vector prepared with R.
In-GAVsv [117] Detection and visualization of structural variation from paired-end mapping data and detection of larger insertions and complex variants with lower false discovery rate Identification of different types of SVs, including large indels, inversions, translocations, tandem duplications and segmental duplications. A FASTA formatted reference sequence and a SAM alignment are required
A PTT formatted annotation file for the reference sequence is optional.
Distinction between homozygous and heterozygous variants
Meander [118] It is mainly developed to visually discover and explore structural variations in a genome based on Read-Depth and Pair-end information Linear view It supports its own file format both for RD and paired-end data
Hilbert curve –based view
Comparison between up to four samples against a reference simultaneously
Visualization ofvarious types of structural inter/intra chromosomal variations
Exploration of data at different resolution levels
MEDEA [119] Genomic feature densities and genome alignments of circular genomes Customization of since tracks can by dragging and dropping into a desired position It supports its own file format
User-defined color schemes
Zooming into specific regions and smooth navigation
MizBee [120] Synteny browser for exploring conservation relationships in comparative genomics data Side-by-side linked views and data visualization at different scales, from the genome to the gene Edge hustling and layering to increase visual signals about conservation relationships related to closeness, size, relationship, and orientation.
Seevolution [121] Interactive 3D environment that enables visualization of diverse genome evolution processes Interactive animation of mutation histories involving genome rearrangement, point mutation, recombination, insertion and deletion. Accepts complete phylogenetic trees and allows path tracing between any two points.
•Simultaneous visualization of multiple organisms related by a phylogeny.
•3D models of circular and linear chromosomes
Sybil [122] Comparative genome data, with a particular importance on protein and gene clustered data Graphical demonstration of local alignment of the genomes in which the clustered genes are located Genomes are organized in a vertical heap, as in multiple alignments and shaded areas links are used to connect genes that belong to the same cluster
VISTA [123] Global DNA sequence alignments of arbitrary length Global and alignment visualization up to several megabases under the same scale Dynamic and interactive dot-plots