Computer based screening of endogenous retrovirus or rt like sequences from the mouse genome project database

Saratha Thevi Thrichelvam, (2005) Computer based screening of endogenous retrovirus or rt like sequences from the mouse genome project database. Universiti Malaysia Sabah. (Unpublished)

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Abstract

In this study the reverse transcriptase gene is studied as it shows the most conserved motif in each domain. Two probes namely Mouse Mammary Tumor Virus (MMTV) and Mus Dunni Endogenous Virus (MDEV) are used to screen the mouse genome database. The four main steps involved in this study are obtaining sequences which act as probe, screening sequences inside the mouse genome database, sequence alignment and finally constructing a phylogenetic tree. A total of 100 sequences that have all the entire domain of reverse transcriptase gene have been successfully screened from mouse genome database. Only 16 sequences are selected from 100 sequence that have been screened based on several criteria for sequence alignment. This selected sequence is then aligned manually and using computer software Clustal W program. Two phylogenetic trees were constructed to study the connection of sequences from mouse endogenous retrovirus and also to investigate the relationship with 7 established genera of retroviruses with viruses obtained from this study. The major result of this study indicate that the endogenous retroviruses are present more in germ line which has 63 sequences compared to 37 sequences in autosome chromosome in both MMTV and MDEV probe. The data presented through this study suggest that endogenous retroviruses are distributed in 19 autosome and 1 sex mouse chromosome. Furthermore tIus tree support previous categorization where MMTV belong betaretroviruses genera and MDEV belongs to gammaretroviruses genera. From both phylogenetic trees, the sequences are classified according similarities in the reverse transcriptase gene.

Item Type: Academic Exercise
Uncontrolled Keywords: Biotechnology , Screening Of Endogenous Retrovirus , RT Like Sequences , Sequence Alignment , Phylogenetic Tree Of Mouse Genome
Subjects: Q Science > QD Chemistry
Divisions: SCHOOL > School of Science and Technology
Depositing User: MDM FAUZIAH MATSIN
Date Deposited: 26 Sep 2013 04:01
Last Modified: 17 Oct 2017 03:29
URI: http://eprints.ums.edu.my/id/eprint/7093

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