On-SOMA

On-SOMA is the online version of our tool to automatically place genomic sequences on an optical restriction map. The techniques used in the tool were specifically designed with the characteristics of short-read sequencing in mind and have been shown to be robust to sequencing errors, misassemblies and fragmented assemblies.

What is an Optical Map? Optical maps are restriction maps generated by a technique called Optical Mapping (developed in the Schwarz lab) where in addition to the sizes of the restriction fragments (pieces of DNA that result upon digestion by a restriction enzyme) their order is also known. For more details about this technology see OpGen Inc. (a commercial provider of optical maps).

For more information on this subject and a description of the algorithms employed by On-SOMA see:

Niranjan Nagarajan, Timothy D. Read and Mihai Pop. Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics (2008)

If you want to ...

Try the online version, visit the Scaffold Sequences Online tab.
Download the source code for the package, visit the Download Package tab.
For programs to use multiple optical maps and combining assembly information with optical maps, email niranjan [AT] umiacs.umd.edu

Why use it?

Soma is the word for wine/intoxicating beverage in many indic languages ... so go ahead try it.
Alternately, you want to quickly put the little pieces of your genome (contigs) into one large piece (scaffold).

Contact Us

For questions/suggestions or to report bugs email niranjan [AT] umiacs.umd.edu

Acknowledgements

This project is supported by Department of Defense Transformational Medical Technologies initiative IB06RS002.