Multiple Comparative Genome Viewer (MCGV)
Multiple Comparative Genome Viewer (MCGV) is a visualization tool for multiple whole genome eukaryotic alignments. MCGV was developed as part of the NIH Comparative Genomics Resource (CGR), which facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.
Alignment Data
MCGV displays multiple whole genome alignments provided by the community. The default view currently shows an alignment of eutherian mammal assemblies generated by Ensembl using the EPO method. Assemblies are aligned relative to an anchor assembly, which is human GRCh38.p14 in this case. We have pre-filtered some assemblies in the original Ensembl data from the MCGV view due to low quality.
You can also use the Alignment Data menu to view an eight-way ape genome alignment from the T2T consortium, as well as an alignment of 137 VGP bird assemblies, or additional alignments generated in-house using the Progressive Cactus pipeline. We will be adding more whole genome alignment data in the coming months. If you know of an alignment that you would like to display in this tool, please get in touch.
Alignments are processed to filter out short alignments and merge adjacent segments. In addition, only best-placed alignments at each location at retained.
Navigating MCGV
Chromosome overview
To navigate to a particular gene in the anchor assembly, start typing a gene name in the Search box. Press Enter or select a suggestion from the dropdown list to navigate to the gene of interest.
The Chromosome overview graph depicts the number of assemblies with alignments at each region of a chromosome on the anchor assembly (e.g. human GRCh38.p14). The alignment data underlying this graph were grouped into fixed-size genomic intervals (e.g., 100kb) called "bins". An assembly is considered ‘aligned’ if it contains any aligned segment to the anchor assembly within the nucleotide range of the bin. Drag across a range of the chromosome overview graph to zoom the view to that location. You can also use the dropdown menu to navigate to a different chromosome in the anchor assembly.
The coordinate range displayed in the Assembly alignments and Sequence conservation sections of MCGV will update automatically when you select a gene from the gene search or change the selected chromosome or chromosome region from the Chromosome overview panel. The selected range in the Chromosome overview graph also updates as you pan and zoom in the Assembly alignments section.
Use the Filter assemblies menu to refine which taxa or assemblies from the alignment you would like to include in the view. The Chromosome overview graph updates when changes are made in this menu or when assemblies are hidden from the Assembly alignments and Sequence conservation panels.
Assembly alignments
The Assembly alignments section displays alignment segments for each assembly depicted as rectangular blocks. MCGV filters the alignment data to display the best-placed alignments of each assembly at each location on the anchor assembly. In cases where the anchor assembly contains a duplication or paralog expansion relative to another assembly, the same coordinate range in the assembly with fewer copies may appear multiple times at different locations relative to the anchor assembly. If the Switch anchor assembly button is active, you will have the option to change the view to a different anchor assembly.
Hide assemblies from view by clicking on the X on the right side of each row. You can also use the Filter assemblies menu to refine which assemblies from the selected dataset you would like to show. Hiding assemblies from the Assembly alignments section will also update the data in the Chromosome overview and Sequence conservation panels. Note that the anchor assembly cannot be hidden.
To view alignments in a compact format, use the Compressed/Default view switch button located to the right of the Undo button. In compressed view, all alignments for each assembly are displayed in a single row, allowing more assemblies to fit within the visible area of the screen. The gene track is available only for the anchor assembly. Additionally, you can resize the species label column by dragging its edge to shrink or expand it to customize the display.
To change the color of alignments, click the Color by menu and choose a color method from the dropdown list. Select the Show legend checkbox to display the alignment color legend. There are three color methods available in the chromosome/gene level views:
- Color by identity – By default, alignment segments are colored by their sequence identity to the anchor. Darker shades of blue represent segments with higher similarity. Identity is calculated across the entire segment and derived from the underlying assembly alignment.
- Color by orientation – Alignment segments are colored based on their orientation, where reverse alignments are shown in purple and forward alignments in grey. The anchor sequence is always in the forward orientation.
- Color by chromosome – Alignment segments are colored according to the coverage rank, which measures how extensively each chromosome aligns to the anchor chromosome. Rank 1 (dark brown) indicates the best-matching chromosome, rank 2 (peach) the second-best, rank 3 (amber) the third-best, and rank 4+ (light gray) includes all remaining chromosomes. These rankings are computed separately for each anchor chromosome and independently across aligned assemblies. In compressed view, this color scheme highlights large-scale genome rearrangements such as translocations and inversions.
Click on an alignment segment to show an info box with more details, including the segment size, exact coordinates, and identity to the anchor assembly. You can choose to zoom the viewer to the range of the alignment. You can navigate to the region of the alignment in NCBI’s GDV genome browser for more detailed analysis of gene structure and sequence.
Gene annotation is displayed under the alignments as green bars. Annotation is provided, where available, from Refseq or from the submitters of the genome assembly. A "jagged" edge is drawn on the end of an exon to indicate that annotation on the assembly extends past the annotation in the aligned region. Click on the gene to view a box with the name, description, and link to NCBI's Gene record page.
The Download option allows you to download:
- An SVG image of your current view that is suitable for use in presentations and publications (available for the default and compressed views at chromosome, gene, and sequence zoom levels).
- A FASTA alignment sequence of up to 200 kb of alignment length. The downloaded FASTA alignment is reference-free; i.e. gaps may be present in the anchor assembly. There may be multiple FASTA in the file for each assembly if there are non-contiguous alignments from the same assembly. FASTA downloads from some alignment datasets may designate repeats in lower case nucleotides.
To navigate in the alignment:
- use the ZOOM and PAN buttons
- drag the viewer to pan left or right
- select a region by dragging over the coordinate ruler of the anchor row
- single click on a gene (green rectangle) to open an info with a Zoom to Gene option
- double click on a gene to zoom to the gene directly
- use the UNDO button to return to the previous view(s); UNDO works for all navigation steps, as well as for chromosome, color, or anchor changes.
Sequence conservation
The Sequence conservation graph is available when the view is zoomed below 1,000,000 bp (1 MB). This graph shows the proportion of alignment that is perfectly matched to the anchor (dark blue) versus divergent (i.e. contains mismatches or gaps) (light blue). The height of the graph represents the number of assemblies with alignment at each location; the white space is the proportion of assemblies that are not aligned. Divergence is calculated as a proportion of mismatched or gapped sequence across a coordinate range (bin).
Drag the graph to pan the view or drag over the ruler to zoom. The bin size is larger when zoomed out; as the view zooms in further, the bin size decreases until the data is calculated and displayed per nucleotide. The Sequence conservation graph zooms and pans synchronously with the Assembly alignments.
Hover over and click on any bin to show an info box that reports the number of assemblies aligned at that location and a species tree of these assemblies. Occasionally, the height of the bin in the graph may not exactly correspond to the reported number of assemblies. This is because the bin range might contain gaps in the alignment. For example, while 33 assemblies may be aligned at some location within a bin, only 27 assemblies may align at any given position; in this case, the bin height in the graph will be 27, while the info box will report 33 assemblies.
When you have zoomed to a region on the anchor where not all assemblies are aligned, you will see a message above the graph giving you the option to hide assemblies without alignment from view. When you select this option, these assemblies will be removed from the Chromosome overview, the Sequence conservation graph, and the Assembly alignments. The assemblies will remain hidden as you navigate around the viewer and can be added back using the 'Show all' option.
Sequence level view
Zoom in as far as you can and you will be able to view aligned nucleotide sequences. Note that this view includes shorter alignment segments that may have been filtered out when zoomed further out. Nucleotide bases are shown as letters A, C, G, or T for the anchor assembly. For other assemblies, matches, mismatches, gaps, and insertions are rendered as described in the legend:
Click on a position in the alignment to open an info box displaying the corresponding coordinate in the aligned assembly along with additional metadata. For insertions, the box also displays the insertion length and sequence (up to 22 nucleotides shown) and allows you to copy the entire insertion sequence for further analysis. Use the View in GDV link to open the genome assembly in the Genome Data Viewer zoomed to the location you are currently viewing.
When zoomed to the sequence, the Sequence conservation graph is replaced by a conservation table. The conservation table summarizes all matches, mismatches, gaps, and insertions for each position in the alignment. Click on a number in the table to see the assemblies underlying the data in a pop-up information box. Within this box, the links Show only these assemblies and Hide these assemblies allow you to filter assemblies at a given alignment position, displaying or hiding those that contain matches, mismatches, gaps, or insertions. If the links are not immediately visible (typically when an alignment includes many assemblies), use the Collapse/Expand option or scroll down within the pop-up box. To return to the complete, unfiltered view, click the Show All link.
The Future
Multiple Comparative Sequence Viewer (MCGV) is in active development. We hope to provide the choice of additional datasets in the coming months. Please contact us if you would like to provide feedback on our work.