SeqMap – A Tool For Mapping Millions Of Short Sequences To The Genome

SeqMap is a tool for identifying viral integration sites from LAM-PCR and LM-PCR analysis. The tool will extract vector sequence data then search existing genome databases for matches to the unique sequences generated by the LAM or LM-PCR reaction. SeqMap displays the vector insertion site graphically, showing the chromosome location and distance to surrounding genes. The tool also allows you to organize your data and make notations.

SeqMap was developed at the Indiana University School of Medicine in the laboratory of Dr. Sean Mooney in collaboration with Drs. Mary Dinauer and Kenneth Cornetta. Development was supported, in part, through a Program Project Grant to Dr. Dinauer (NHLBI P01 HL053586), the National Gene Vector Laboratory (NCRR U42 RR11148), and the Indiana Genomics Initiative (INGEN). The SeqMap tool will now be hosted by the National Gene Vector Biorepository funded through the National Center for Research Resources.

Availability and Implementation: The method is implemented in a publicly accessible web server platform, SeqMap 2.0, containing analysis tools and both private and shared lab workspaces that facilitate collaboration among researchers. Available at

SeqMap is open to all, but access to the web interface requires a log-in so that you can continue to access your data over time.

Hawkins TB, Dantzer J, Peters B, Dinauer M, Mockaitis K, Mooney S, Cornetta K. (2011)

Identifying viral integration sites using SeqMap 2.0. Bioinformatics 27(5), 720-22. [abstract]