Computer-based screening of piscine endogenous retrovirus from Pufferfish Genome Project Database

Malaty Sinniah, (2005) Computer-based screening of piscine endogenous retrovirus from Pufferfish Genome Project Database. Universiti Malaysia Sabah. (Unpublished)

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Abstract

The main purpose of this study is to determine the existence of endogenous retrovirus in Pufferfish genome through screening the Pufferfish Genome Database. In this study, the reverse transcriptase portion of pol gene was examined as it exhibits the most sequences containing highly conserved motif. Four major steps that were carried out in order to fulfill the objectives were data mining of probe, screening, sequence alignment and phylogenetic tree construction. Probe sequences were screened in Pufferfish Genome Database through Fugu Genome Blast Search. Three sequences containing conserved motif of domains of reverse transcriptase gene in retrovirus were assembled as the preliminary result of this project. About 371 sequences were screened through the blast search. Continuous screening of all eight probe sequences enabled the assembly of 65 sequences. Out of that number, 18 sequences were selected for sequence alignment and phylogenetic tree construction. The sequences obtained through Blast Search were then aligned as it exhibits the highly conserved motif of all domains of reverse transcriptase gene in retroviruses. This was to detect the relationship between the established sequences within fish database and the newly gathered sequences. The Phylogenetic tree that was built to study the relationships between different species of organism. The phylogenetic tree revealed the grouping pattern of seven main genera of retroviruses and the relationships between the genera.

Item Type: Academic Exercise
Uncontrolled Keywords: endogenous retrovirus, Pufferfish genome, Database, genera, phylogenetic tree, Fugu Genome Blast Search
Subjects: Q Science > QH Natural history > QH301 Biology
Divisions: SCHOOL > School of Science and Technology
Depositing User: MDM SITI AZIZAH IDRIS
Date Deposited: 20 Jan 2014 06:05
Last Modified: 10 Oct 2017 08:47
URI: http://eprints.ums.edu.my/id/eprint/8026

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