MouseIndelDB: a database integrating genomic indel polymorphisms that distinguish mouse strains

Abstract

MouseIndelDB is an integrated database resource containing thousands of previously unreported mouse genomic indel (insertion and deletion) polymorphisms ranging from approximately 100 nt to 10 Kb in size. The database currently includes polymorphisms identified from our alignment of 26 million whole-genome shotgun sequence traces from four laboratory mouse strains mapped against the reference C57BL/6J genome using GMAP. They can be queried on a local level by chromosomal coordinates, nearby gene names or other genomic feature identifiers, or in bulk format using categories including mouse strain(s), class of polymorphism(s) and chromosome number. The results of such queries are presented either as a custom track on the UCSC mouse genome browser or in tabular format. We anticipate that the MouseIndelDB database will be widely useful for research in mammalian genetics, genomics, and evolutionary biology. Access to the MouseIndelDB database is freely available at: http://variation.osu.edu/.

Figure 1.

MouseIndelDB user interface. Two query modes are available at the home page of the MouseIndelDB web interface. Users can alternatively focus upon local features of interest, or search the database in categories according to mouse strain(s), class of indel polymorphism(s) and chromosome number. Default entries and other examples of optional user inputs are provided.

Figure 2.

MouseIndelDB custom track at UCSC mouse genome browser. Polymorphic SINE and L1 retrotransposons at a region of mouse chromosome 1 are shown on the MouseIndelDB custom track displayed at the UCSC mouse genome browser (mm9 assembly). Three WGS sequence traces from DBA/2J mice each skip over a single polymorphic SINE retrotransposon, present in the reference (designated as REF-IN) genome but absent from DBA (top, labeled as REF-IN, red rectangles, trace IDs 1090731691, 1101700443 and 109988639). The reference SINE element can be seen on the conventional RepeatMasker track (bottom). In addition, a nearby mapped sequence trace from the 129X1 strain indicates an insertional polymorphism present in that alternative (ALT-IN) strain but absent from the reference C57 genome (blue rectangle, labeled as ALT-IN, trace ID 1073424193). In the latter case, a 50-nt thin projection (thin blue rectangle, right) indicates the genomic junction and relative position of the previously unreported L1 retrotransposon integrant in the 129X1 genome. Superimposed arrows indicate the direction of sequence trace alignments compared with the reference genome.