## Abstract

DNA sequence can be defined as a succession of letters, representing the order of nucleotides within DNA, using a permutation of four DNA base codes including adenine (A), guanine (G), cytosine (C), and thymine (T). The precise code of the sequences is determined using DNA sequencing methods and technologies, which have been developed since the 1970s and currently become highly developed, advanced and highly throughput sequencing technologies. So far, DNA sequencing has greatly accelerated biological and medical research and discovery. However, in some cases DNA sequencing could produce any ambiguous and not clear enough sequencing results that make them quite difficult to be determined whether these codes are A, T, G, or C. To solve these problems, in this study we can introduce other representation of DNA codes namely Quaternion Q = (P_{A}, P_{T}, P_{G}, P_{C}), where P_{A}, P_{T}, P_{G}, P_{C} are the probability of A, T, G, C bases that could appear in Q and P_{A} + P_{T} + P_{G} + P_{C} = 1. Furthermore, using Quaternion representations we are able to construct the improved scoring matrix for global sequence alignment processes, by applying a dot product method. Moreover, this scoring matrix produces better and higher quality of the match and mismatch score between two DNA base codes. In implementation, we applied the Needleman-Wunsch global sequence alignment algorithm using Octave, to analyze our target sequence which contains some ambiguous sequence data. The subject sequences are the DNA sequences of Streptococcus pneumoniae families obtained from the Genebank, meanwhile the target DNA sequence are received from our collaborator database. As the results we found the Quaternion representations improve the quality of the sequence alignment score and we can conclude that DNA sequence target has maximum similarity with Streptococcus pneumoniae.

Original language | English |
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Title of host publication | International Symposium on Current Progress in Mathematics and Sciences 2016, ISCPMS 2016 |

Subtitle of host publication | Proceedings of the 2nd International Symposium on Current Progress in Mathematics and Sciences 2016 |

Editors | Kiki Ariyanti Sugeng, Djoko Triyono, Terry Mart |

Publisher | American Institute of Physics Inc. |

ISBN (Electronic) | 9780735415362 |

DOIs | |

Publication status | Published - 10 Jul 2017 |

Event | 2nd International Symposium on Current Progress in Mathematics and Sciences 2016, ISCPMS 2016 - Depok, Jawa Barat, Indonesia Duration: 1 Nov 2016 → 2 Nov 2016 |

### Publication series

Name | AIP Conference Proceedings |
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Volume | 1862 |

ISSN (Print) | 0094-243X |

ISSN (Electronic) | 1551-7616 |

### Conference

Conference | 2nd International Symposium on Current Progress in Mathematics and Sciences 2016, ISCPMS 2016 |
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Country | Indonesia |

City | Depok, Jawa Barat |

Period | 1/11/16 → 2/11/16 |