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

Keiko Akagi; Robert M. Stephens; Jingfeng Li; Evgenji Evdokimov; Michael R. Kuehn; Natalia Volfovsky; David E. Symer

doi:10.1093/nar/gkp1046

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

Keiko Akagi, Robert M. Stephens, Jingfeng Li, Evgenji Evdokimov, Michael R. Kuehn, Natalia Volfovsky, David E. Symer

Research output: Contribution to journal › Article › peer-review

19 Scopus citations

Abstract

MouseIndelDB is an integrated database resource containing thousands of previously unreported mouse genomic indel (insertion and deletion) polymorphisms ranging from ~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/.

Original language	English (US)
Article number	gkp1046
Pages (from-to)	D600-D606
Journal	Nucleic acids research
Volume	38
Issue number	SUPPL.1
DOIs	https://doi.org/10.1093/nar/gkp1046
State	Published - Nov 20 2009
Externally published	Yes

ASJC Scopus subject areas

Genetics

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abstract = "MouseIndelDB is an integrated database resource containing thousands of previously unreported mouse genomic indel (insertion and deletion) polymorphisms ranging from ~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/.",

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AU - Stephens, Robert M.

AU - Li, Jingfeng

AU - Evdokimov, Evgenji

AU - Kuehn, Michael R.

AU - Volfovsky, Natalia

AU - Symer, David E.

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

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ASJC Scopus subject areas

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