SeqMap 2.0   Login About

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.



January 2011 -- All of the recent updates to SeqMap have been published with open access in Bioinformatics. Click here to read the article.


July 2010 -- Barcode sequences used to mark sequences to be analyzed can now be provided by the user, to be masked out during processing. These sequence sets can be uploaded or copy/ pasted into a text box, much like the vector sequences. If the submitted data is analyzed as a high-throughput batch, resulting genomic sequences will be grouped by barcode before consensus sequences are created, so as to identify similar hits in multiple samples.

Users may now submit data without logging in if they so choose. A valid email address is needed to provide notification when processing completes. The one-shot submission page can be found here.


November 2009 -- The SeqMap pipeline has been redesigned to accommodate high throughput sequencing results, while still maintaining its original functionality. Users can now copy/ paste or upload their FASTA formatted sequences and choose whether to create consensus sequences based on preliminary BLAT results and run this subset through the analysis pipeline, or to run each input sequence separately.

In addition to this major change, logins can now be utilized on a per-person basis. Each user may create a separate login, and either create a new lab/ project space for data, or be connected to already-existing lab/ project spaces. For now, granting access to old data for new users will be handled by the SeqMap Admin.

SeqMap Sample Page

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.

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. Click here to obtain a log-in. If you wish to provide a single set of data for analysis without logging in, the submission page can be found here. You can also review a SeqMap demonstration site by logging in with the case sensitive username "demo" and password "demo".

(Note: currently the SeqMap and NGVB log-ins are maintained differently, so that you must register with each. We hope to simplify the log-in procedure over the coming months and we will notify registered users when that change occurs).


For more information on the NGVB, go to

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Indiana University School of Medicine | Department of Medical and Molecular Genetics | Indiana Genomics Initiative
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