MouseIndelDB

MouseIndelDB catalogs mouse insertion and deletion (indel) polymorphisms to provide a reference of structural variation in laboratory mouse genomes.

Key Features:

• Catalog content: Contains thousands of previously unreported insertion and deletion polymorphisms identified in laboratory mouse strains.
• Indel size range: Records cover polymorphisms approximately 100 nucleotides (nt) to 10 kilobases (Kb) in length.
• Sequence source: Built from 26 million whole-genome shotgun sequence traces derived from four laboratory mouse strains.
• Mapping method: Sequence traces were aligned to the C57BL/6J reference genome using GMAP to identify and catalog indels.
• Local query options: Supports searches by chromosomal coordinates, nearby gene names, or other genomic feature identifiers.
• Bulk query options: Enables bulk retrieval by specific mouse strains, classes of polymorphisms, and chromosome numbers.
• Output formats: Query results can be exported as a custom track for the UCSC Mouse Genome Browser or as tabular data.

Scientific Applications:

• Mammalian genetics: Reference for locating structural variants within laboratory mouse strains for genotype–phenotype studies.
• Genomics and variant annotation: Resource for annotating insertion and deletion polymorphisms in comparative and functional genomic analyses.
• Evolutionary biology: Dataset for studying patterns of genomic evolution and structural variation among mouse strains.

Methodology:

Aligned 26 million whole-genome shotgun sequence traces from four laboratory mouse strains to the C57BL/6J reference genome using GMAP to identify and catalog insertion and deletion polymorphisms (~100 nt to 10 Kb).