Igv Genome Viewer Download

GDV supports the exploration and analysis of NCBI-annotated and selected non-NCBI annotated eukaryotic genome assemblies. Currently, assemblies from over 2580 organisms are available.

To view more organisms in the tree, click on nodes that have '+' signs. Press and hold the '+' to expand and reveal all the subgroups.

Or, search for an organism using the search box above.

New! Click on Switch view at the top to see another way of navigating genomes.

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Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

The Ensembl Rapid Release website provides annotation for recently produced, publicly available vertebrate and non-vertebrate genomes from biodiversity initiatives such as Darwin Tree of Life, the Vertebrate Genomes Project and the Earth BioGenome Project.

The Comparative Genome Viewer (CGV) is a visualization tool that helps you quickly compare two genomes based on assembly-assembly alignments provided by NCBI. CGV includes eukaryotic (animal, plant and fungal) assemblies, and many cross-species comparisons. You can view chromosome-scale rearrangements, search for genes, and display aligned regions at the sequence level.

This online, interactive workshop is designed for any life scientist, including research students and educators, who want to visually compare genomes to gain biological insight and share these insights with others. Some familiarity with genomics vocabulary and concepts is recommended for attendees.

[ back to top ]What is the Genome ViewerThe GViewer provides users with a complete genome view of genes, QTLs and strains annotated to a function, biological process, cellular component, phenotype, disease or pathway term. The tool will also search for matching terms from the Gene Ontology, Mammalian Phenotype Ontology, Disease Ontology or Pathway Ontology.

The availability of multiple annotated mouse genome assemblies serves as a foundation for investigating the genomic and genetic basis for phenotype diversity across inbred and wild-derived strains of laboratory mice (Keane et al. 2011; Lilue et al. 2018; Thybert et al. 2018). However, even with the availability of widely used genome browsers, interactive and customizable comparison of annotated genome features and their organization across multiple genomes remains a significant barrier to accessing and exploring these genomes. Here we describe the multiple genome viewer (MGV) which we developed to support interactive exploration and visualization of genome annotations for multiple lines of laboratory mice and for easy access to the sequence data for these annotations for alignment and data analysis. MGV relies on the mouse genome assemblies available from the Ensembl genome browser. The genome feature annotations displayed in MGV come from the mouse genome database (MGD) unified gene catalog (Zhu et al. 2015). The MGD unified gene catalog combines genome feature predictions from Ensembl/GenCode and NCBI into a single non-redundant annotation set which serves as the foundation for the expertly curated phenotype, function, and developmental expression annotations for mouse genes available from MGD and the gene expression database (GXD) (Baldarelli et al. 2021; Blake et al. 2020; Zhu et al. 2015) Although the implementation for MGV reported here is focused on mouse genomes, the software is genome agnostic and was designed to accommodate multiple annotated genomes from any organism and can also support the display of homologous genome features across different organisms.

To represent genome features of multiple strains, MGD uses the concept of a canonical genome feature (Fig. 1A). A canonical genome feature is one that exists in any strain or species of Mus. In MGD, any genome feature that has a unique, permanent MGI accession id is a canonical feature. Canonical gene records are linked to instances of the genome feature found in the genome of different Mus strains and species. The canonical genome feature concept supports rapid identification of strain-specific genome features and the capacity to associate biological annotations with specific strains. MGD provides a tabular summary of the strain distribution of genome features along with their strain-specific identifiers and genome coordinates (Fig. 1B).

Canonical genes are the abstract representations of any/all identified mouse genome features regardless of strain. A Canonical genes have MGI accession ids and official nomenclature and historically have been the entities associated with biological annotations about function, phenotype, and disease. With the advent of multiple mouse genome assemblies, the concept of a strain gene was added to support robust representation of strain-specific genome annotations and attributes. Strain genes have strain-specific accession identifiers and genome coordinates. A given canonical mouse gene may or may not exist in a specific mouse strain, as shown for Mx2 (MGI:97244), which has not been annotated in the AKR/J inbred strain. B The strain distribution table for the Mx2 gene showing the strain-specific identifiers and genome locations. This table is available from the gene detail page in MGD. The Mx2 gene is a polymorphic pseudogene meaning the gene codes for a functional protein in some strains, but not others

The user interface for MGV consists of a control panel, tracks for displaying genome feature maps of user-selected genomes, and a genome-wide overview (Fig. 2). The control panel on the left side of the display comprises several modules that allow users to control which genomes and features to display, options to modify display properties, controls for downloading sequences, and the ability to create and display lists of features. The basic functions for MGV are described below. The MGV user guide lists the key and mouse driven commands for the interface and can be invoked at any time while using the software with the H command.

By design, MGV has no predefined reference genome; any genome can be selected as the reference, which then determines which regions are shown for other displayed genomes. Selecting a reference genome is optional; however, other modes support aligning the genomes around common landmarks, or even using each displayed genome as an independently scrollable and zoomable browser.

The genome features displayed in MGV can be toggled on and off according to multiple criteria, including feature biotype (i.e., protein coding, pseudogene, etc.), feature length, features present in some displayed genomes but not others, and features that have been selected by the user.

A powerful feature of MGV is the ability to select and download sequences from displayed genomes. Selecting sequences adds descriptors to a sequence cart which functions like an online shopping cart. From the sequence cart, researchers can download the sequences for their selected genome features in FASTA format to a file, browser tab, or to the clipboard. Because the sequence cart contains only descriptors, there is no limit to the number of sequence features listed there. However, a single download operation is limited to a maximum of 100 MB and 4000 sequences.

The primary driver for the development of MGV was to allow researchers to visualize and explore genome features and their organization across different mouse genomes. The use cases described below are examples for two of the main uses of MGV: exploring annotation similarities and differences across the genomes of multiple mouse strains and comparing the organization of homologous genome features from different organisms.

While most of the available mouse genomes have the Fem1a gene located on chromosome 17, this gene is currently annotated on chromosome 11 in strains BALB/cJ and FVB/NJ. Most strains have a Fem1a-related gene (Fem1al; MGI: 2441689) annotated on chromosome 11, but for several strains (129S1/SvImJ, C57BL/6NJ, LP/J, WSB/EiJ) the Fem1al gene is annotated to chromosome 17 (data not shown). The sequence gaps in the genome assemblies identified using the MGV on chromosome 17 will need to be resolved before the relationships between Fem1a-related sequences on chromosomes 11 and 17 across different mouse strains can be fully and accurately characterized.

The strain distribution of the Cwc22 gene (CWC22 spliceosome-associated protein; MGI:2136773) illustrates a difference in annotation across mouse strains that is the result of evolutionary divergence as opposed to technical issues with genome sequence quality and completeness. Cwc22 is annotated in all of the available mouse strain genomes with the exception of the Spretus/EiJ genome (Fig. 5). The gene is contained within the R2d segmental duplication region of the mouse genome (Morgan et al. 2016). We aligned a transcript of the Cwc22 gene from C57BL/6J to the Spretus/EiJ genome using Splign and revealed the existence of a remnant of the gene in Spretus with significant sequence decay (Fig. 5). Future updates of genome features in the Spretus/EiJ genome should include the annotation of a Cwc22 pseudogene.

A MGV aligned view of the Cwc22 gene showing the missing annotation in Spretus/EiJ. B NCBI Splign alignment of the Cwc22 transcript from C57BL/6J to the Spretus/EiJ genome reveals a remnant of the Cwc22 gene in Spretus with severe evolutionary decay in the sequence

MGV supports the exploration of the genome context of orthologous genes from different organisms. For example, there are two mouse orthologs of the human THOC2 gene (THO Complex 2; HGNC:19073): Thoc2 (MGI:2442413) and Thoc2l (MGI:3040669) located on chromosomes X and 5, respectively (Fig. 6). The human THOC2 gene is associated with the disease X-linked intellectual disability-short stature-overweight syndrome (DOID:0112056; OMIM #300957). Aligning the MGV display on human THOC2 produces a useful split view of the two mouse orthologs (Fig. 6). MGV does this automatically for all orthologs of a selected feature in the genomes displayed where orthologs in a given comparison genome are present on different chromosomes or located outside of the rendered view. It is clear from the genome context that the mouse chromosome X locus is in a region of conserved synteny with respect to human THOC (Fig. 6A). ff782bc1db