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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 HAMDANI1,2 & MOHD FIRDAUS-RAIH1*
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
Diserahkan: 21 September 2017/Diterima:
15 Mac 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 RUJUKAN
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*Pengarang untuk
surat-menyurat; email: firdaus@mfrlab.org
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