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Fuzzy-based Spectral Alignment for Correcting DNA Sequence from Next Generation Sequencer

Journal from gdlhub / 2016-11-07 02:01:33
Oleh : Kana Saputra S, Wisnu Ananta Kusuma, Agus Buono, Telkomnika
Dibuat : 2016-06-01, dengan 1 file

Keyword : DNA Sequencing Errors, Fuzzy Inference System Model, Next Generation Sequencing, Spectral Alignment Method
Url : http://journal.uad.ac.id/index.php/TELKOMNIKA/article/view/2395

Next generation sequencing technology is able to generate short read in large numbers and in a relatively short time in single running programs. The graph based DNA sequence assembly, that is used to handle these big data in assembly step, is very sensitive to DNA sequencing errors. This problem can be solved by performing an error correction step beforethe assembly process. This research proposed fuzzy inference system based spectral alignment method which can detect and correctDNA sequencing errors. The spectral alignment method was implemented asa pre-processing step before the DNA sequence assembly process. The evaluation was conducted using Velvet assembler. the total nodes yielded by the Velvet assembler become a measure ofthe success of error correction. The results showed that the fuzzybased spectral alignment method generated small total nodes for k = 53. It was concluded that the fuzzybased spectral alignment method is successfully able to detect and correct DNA sequencing errors.

Deskripsi Alternatif :

Next generation sequencing technology is able to generate short read in large numbers and in a relatively short time in single running programs. The graph based DNA sequence assembly, that is used to handle these big data in assembly step, is very sensitive to DNA sequencing errors. This problem can be solved by performing an error correction step beforethe assembly process. This research proposed fuzzy inference system based spectral alignment method which can detect and correctDNA sequencing errors. The spectral alignment method was implemented asa pre-processing step before the DNA sequence assembly process. The evaluation was conducted using Velvet assembler. the total nodes yielded by the Velvet assembler become a measure ofthe success of error correction. The results showed that the fuzzybased spectral alignment method generated small total nodes for k = 53. It was concluded that the fuzzybased spectral alignment method is successfully able to detect and correct DNA sequencing errors.

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