Abstract
The assembled and annotated genomes for 16 inbred mouse strains (Lilue et al., Nat Genet 50:1574–1583, 2018) and two wild-derived strains (CAROLI/EiJ and PAHARI/EiJ) (Thybert et al., Genome Res 28:448–459, 2018) are valuable resources for mouse genetics and comparative genomics. We developed the multiple genome viewer (MGV; http://www.informatics.jax.org/mgv) to support visualization, exploration, and comparison of genome annotations within and across these genomes. MGV displays chromosomal regions of user-selected genomes as horizontal tracks. Equivalent features across the genome tracks are highlighted using vertical ‘swim lane’ connectors. Navigation across the genomes is synchronized as a researcher uses the scroll and zoom functions. Researchers can generate custom sets of genes and other genome features to be displayed in MGV by entering genome coordinates, function, phenotype, disease, and/or pathway terms. MGV was developed to be genome agnostic and can be used to display homologous features across genomes of different organisms.
Highlights
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)
The genome feature annotations displayed in multiple genome viewer (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 National Center for Biotechnology Information (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) 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 support the display of homologous genome features across different organisms
Summary
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). 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) 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 support the display of homologous genome features across different organisms
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
