Helicos has developed its own dynamic programming alignment tools optimized for sequences output from the HeliScope™ Single Molecule Sequencer. These non-proprietary tools, which will be made available through Helicos’ open source portal, will enable alignment of the full length of a short sequence fragment (25- to 30-mer) to a long reference sequence without incurring end gap penalties.
For flexibility, Helicos’ alignment tools support three methods of alignment:
- Needleman-Wunsch
- Smith-Waterman
- A “hybrid” type combining features of global and local alignment schemes
Multi-Pass Sequencing Alignment
The Helicos method developed for
multi-pass sequencing mode involves:
- Alignment of the reads to each other to form a consensus;
- Alignment of the consensus to the reference sequence to identify candidate sub-regions of the genome where alignment is likely;
- Decoupling of the individual reads;
- Alignment of the individual reads to the best candidate sub-region;
- Application of a scoring function to select the best alignment.