Scaffolding using Optical Map Alignment

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 process called Optical Mapping (developed in the Schwartz lab) that allows the order of restriction fragments (pieces of DNA that result upon digestion by a restriction enzyme) to be determined, in addition to their sizes. This simple description belies the complex combination of genomic technologies, computational algorithms, and software that make the mapping process possible. For more details check out the papers published by the Schwartz lab.

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.
  • A new version of SOMA is now available. It now contains programs to use multiple optical maps and to combine assembly information with optical maps as well as several refinements to the original package. The web version will be updated soon.

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


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