Search / Alignment / Assembly

Random-permutations-based algorithms can be used for various applications, such are read alignment/mapping and de novo assembly.


Read alignment

An introduction is available “A Random-Permutations-Based Approach to Fast Read Alignment”  ( RECOMB-SEQ 2013 paper).

Also see [Charikar, 2002] (random permutations in search without the special properties for the sequencing problem), and this report on the properties of sequencing.

Another technical report describes different implementations and extensions to the algorithms.


These are some frequently asked questions about the algorithm and prototype.

A prototype DNA read aligner will be available upon request for non-commercial use in academia. For more information, please contact us.



A technical report about using permutations-based algorithms for assembly, error-correction and other applications is available here.