Sains Malaysiana 47(8)(2018): 1731–1739

http://dx.doi.org/10.17576/jsm-2018-4708-12

Analisis dan Penyaringan Data Lewah Interaksi Kelompok Bes Berikatan Hidrogen dalam Struktur RNA 3-Dimensi

(Analysis and Filtering for Redundant Data of Hydrogen-bonded Base Interaction Clusters

in RNA 3-Dimensional Structures)

HAZRINA YUSOF HAMDANI^1,2 & MOHD FIRDAUS-RAIH^1*

¹Pusat Pengajian Biosains dan Bioteknologi, Fakulti Sains dan Teknologi, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

²Institut Perubatan dan Pergigian Termaju, Universiti Sains Malaysia, 13200 Bertam, Kepala Batas, Pulau Pinang, Malaysia

Received: 21 September 2017/Accepted: 15 March 2018

ABSTRAK

Susun atur 3-dimensi (3D) yang sama boleh disalah cerap sebagai berbeza dari sudut penglihatan yang berlainan. Bagi makromolekul biologi, permasalahan ini juga dihadapi oleh algoritma pencarian susun atur 3D. Keputusan hasil larian yang sama akan diperoleh berulang kali (data lewah) kerana hasil tersebut boleh mempunyai susun atur jujukan berbeza. Permasalahan ini tidak ditemui di dalam pencarian jujukan. Dalam kajian ini, dua kaedah untuk menyaring data lewah tersebut telah dibangunkan dan dibandingkan iaitu kod Prüfer (berasaskan teori graf) dan kaedah saringan data lewah (dibangunkan secara khusus untuk kajian). Model hasil carian pula adalah menggunakan COnnection tables Graphs for Nucleic ACids (COGNAC) bagi pencarian interaksi kelompok bes berikatan hidrogen. Perbandingan yang dilakukan menunjukkan bahawa kaedah saringan data lewah mampu untuk mengenal pasti dan menyaring antara 50.5% sehingga 80% data lewah daripada hasil larian asal COGNAC berbanding kod Prüfer yang hanya mengenal pasti dan menyaring 50% data lewah daripada hasil larian asal COGNAC. Oleh itu, kaedah saringan data lewah telah diimplementasi ke dalam COGNAC. Selain itu, kaedah saringan data lewah ini juga boleh diguna pakai untuk algoritma yang tidak bergantung kepada jujukan bagi pencarian motif 3D dalam struktur protein.

Kata kunci: COGNAC; interaksi kelompok bes berikatan hidrogen; motif 3D RNA

ABSTRACT

There is a tendency for 3-dimensional (3D) arrangements to appear differently from different viewing angles. In biological macromolecules, this is a problem that is also encountered by algorithms searching for 3D arrangements. This results in the same output being retrieved repeatedly because they are not considered redundant from different points of the search. This is a problem that is not encountered for sequence level searches. In this study, we developed two approaches to filter such redundant data that are the Prüfer code (based on graph theory) and our own redundant data filtering method. The search results model uses the COnnection tables Graphs for Nucleic ACids (COGNAC) algorithm to search for clusters of bases that are connected by hydrogen bonds. The comparison between the two methods showed that the redundant data filtering method developed in this work was able to identify and filter between 50.5% and 80% of the redundant data from the original COGNAC results compared to the Prüfer code that identified and filtered 50% of the redundant data from the original COGNAC results. This redundant data filtering method was then integrated into the COGNAC computer program. Furthermore, the redundant data filtering method can also be deployed to the results of other sequence independent 3D search algorithms including those for protein 3D structures.

Keywords: COGNAC; hydrogen-bonded base interactions clusters; 3D RNA motive

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*Corresponding author; email: firdaus@mfrlab.org