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Kart- Ultra-fast mapping for short and long reads with high error tolerance

Inventor
Hsu Wen-Lian, Lin Hsin-Nan
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Docket Number:05A-1041224

Inventor:Hsu Wen-Lian, Lin Hsin-Nan

IP Status:Pending

 

Abstract:

The invention gives a divide-and-conquer algorithm called Kart, that separates the given sequence into smaller pieces whose alignment can be carried out independently, and their concatenated alignment constitutes the global alignment of the entire sequence. Kart could be viewed as aligning multiple seeds simultaneously in parallel.

 

Fields of Application:

the read mapping of Next-generation sequencing (NGS)

 

Advantages when compared to the existing technologies:

The invention can process long reads as fast as short reads. Furthermore, it can tolerate much higher error rates. The experiments show that Kart spends much less time on longer reads than most aligners and still produce reliable alignments.

 

Contact Person:Ming-Chieh Chen / 886-2-2787-2509 / mingchieh@gate.sinica.edu.tw