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Alignment of Sanger Sequencing reads to reference

Mutation Surveyor, versions 3.97 and forward, employ a unique multi-step alignment algorithm initially developed for our NextGENe software, which utilizes “seed sequences” significantly enhancing the alignment process. Mutation Surveyor, compatible with outputs from all major sequencing platforms, Applied BioSystems’ Prism®, Beckman Coulter CEQ and MegaBACE, utilizes a 4 step process to align sample reads to the reference containing significant INDELS or multiple variants,( up to 20% of the bases). Initial step utilizes a 12 bp seed of the sample sequence moving in single bp steps along the reference, if a mis-match is detected, the software reduces the seed to 6bp and continues. The software automatically switches to a 3bp seed in the event of continued mis-match and finally uses the Smith-Waterman algorithm for local alignment. This technology is a significant improvement over the pair-wise technology used in other programs, such as Variant Reporter™, DNAStar®, or Sequencher® providing robust alignment of sequence traces found even in HIV patients or 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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Mutation Surveyor Capabilities:
Detection Sensitivity & Accuracy
INDEL Detection
INDEL de-Convolution
Somatic Mutation Detection
Mutation Quantification
Methylation Analysis
Hypervariable Region Variant Detection
Reference Assembly
Custom Reporting Options
Alignment of Reads
Mitochondria DNA Sequence Analysis
Base Calling
Unattended Operation 

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