Computer Aided Simulation of DNA Fingerprint Amplified Fragment Length Polymophism (AFLP) Using Suffix Tree Indexing and Data Mining

Prilianti, Kestrilia Rega and Putra, Sulistyo Emantoko Dwi and Whendy, Bhinawan and Budiman, Agung (2011) Computer Aided Simulation of DNA Fingerprint Amplified Fragment Length Polymophism (AFLP) Using Suffix Tree Indexing and Data Mining. In: International Conference on Biological Science Faculty of Biology Universitas Gadjah Mada (ICBS BIO-UGM 2011), September 23-24, 2011, Yogyakarta.

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Abstract

AFLP is one of the DNA Fingerprinting techniques which have broad application as genetic marker in various fields. Begin with the DNA sequence digestion using one or more particular restriction enzyme, ligation of the adapters to the overhanging sticky ends followed by DNA fragments amplification using PCR. The PCR reaction uses primers that match the adapter sequence and have some (1 to 3) dditional “selective” bases which could be any bases, this reduces the number of bands that will be amplified. Such technique intended to increase the amplified fragments peculiarity so the polymorphism of the organism being studied could be well visualized by gel electrophoresis. The computer aided of AFLP simulation developed in this research was aimed to predict this electrophoresis result by simulate the digestion, ligation and PCR process using some pattern recognition algorithm applied to the DNA sequence from online databases. Through this simulation the researcher could determine the best combination of restriction enzyme and selective bases for their laboratory experiment. Suffix tree indexing was conducted during the exploration process of the genome sequence (in FASTA format) to find the restriction sites rapidly and create fragments of it. Data modeling enable the system draws the fragments into virtual DNA’s electrophoresis pattern. Data mining accomplish the simulation by exploring overall possible virtual DNA’s electrophoresis pattern and determine the best restriction enzyme and selective bases combination by calculating certain quantitative criteria.

Item Type:	Conference or Workshop Item (Paper)
Uncontrolled Keywords:	DNA Fingerprint, AFLP, PCR, Suffix Tree Indexing, Data Mining
Subjects:	Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Divisions:	Faculty of Technobiology > Department of Biology
Depositing User:	Kestrilia Rega Prilianti 61150
Date Deposited:	03 Aug 2012 03:42
Last Modified:	09 Jun 2021 03:00
URI:	http://repository.ubaya.ac.id/id/eprint/903

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