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 |