SeqMDD is a tool that efficiently implements reads mapping with an high level of mismatches tolerance thanks to an encoding of the reference genome into Multi-valued Decision Diagrams (MDDs). SeqMDD can be applied to a variety of functional genomics applications, including transcriptome mapping and profiling, ChIP-Seq, as well as SNPs and small indel-type structural variation detection.
SeqMDD takes as input a reference genome, a set of SOLiD sequences, a mismatch level and produces in output, for each SOLiD sequence in input, the list of its positions in the reference genome and the position of the mismatches in the sequence, if any.
SeqMMD runs under Linux/Unix, it is written in C++ and uses the Meedly library to manage MDDs. Meedly was developed at the University of Iowa at Aimes
For a more in-depth introduction to MDD look at:
Symbolic Representations and Analysis of Large Probabilistic Systems
In Validation of Stochastic Systems
2004, pages: 296-338. Springer.For more details about SOLiD technology, see: