Fuzzy-based Spectral Alignment for Correcting DNA Sequence from Next Generation Sequencer
Abstract: 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 before the assembly process. This research proposed fuzzy inference
system based spectral alignment method which can detect and correct DNA
sequencing errors. The spectral alignment method was implemented as a 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 of the success of error correction. The results showed that the
fuzzy-based spectral alignment method generated small total nodes for k = 53.
It was concluded that the fuzzy-based spectral alignment method is successfully
able to detect and correct DNA sequencing errors.
Keywords: DNA Sequencing
Errors, Fuzzy Inference System Model, Next Generation Sequencing, Spectral
Alignment Method
Author: Kana Saputra S
Journal Code: jptkomputergg160186
