Alignment of Sanger Sequencing reads to reference

Mutation Surveyor software employs a unique multi-step alignment algorithm initially developed for our NextGENe software, which utilizes “seed sequences” to significantly enhance the speed and accuracy alignment process. Mutation Surveyor utilizes a four step process to align sample reads to the reference, detecting variants including single nucleotide polymorphisms (SNPs), insertion and deletion (INDEL) events, and low frequency (somatic, mosaic, heteroplasmic) variants. The initial step utilizes a 12bp seed of the sample sequence, moving in single base pair steps to match the sample to the reference. If a mis-match is detected, the software reduces the seed to 6bp and continues alignment. The software automatically switches to a 3bp seed, and if further mis-match is detected, the software employs the Smith-Waterman algorithm for local alignment. This alignment technology provides a significant speed and accuracy improvement over the pair-wise technology used in other programs such as Varaint Reporter™, DNAStar®, or Sequencher®, providing robust alignment and mutation detection found even in hypervariable regions.

Mutation Surveyor software's unique alignment process is capable of aligning sample/patient traces containing significant INDELs and 20% variation from the reference sequence

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