Next Generation Sequence Analysis Of Sequences From Sra File Of Hiv-1 Envelope Protein.
Sahil Sinha, Ganesh Chandra Sahoo, Sindhuprava Rana, RK Topno, Md Yusuf Ansari, Manas Ranjan Dikhit, Rishikesh Kumar, Krishna Panday, Pradeep Das. · Zenodo (CERN European Organization for Nuclear Research) · 2018
Acquired Immunodeficiency Syndrome (AIDS) caused by Human Immunodeficiency Virus is a serious public health concern globally. Therefore, the Next-Generation Sequencing (NGS) analysis is critical elucidating different parts of envelope sequences of Human Immunodeficiency Virus-1 (HIV-1). The Phylogenetic relationships with other viral sex transmitted diseases (STD), bacterial STD, fungal and protozoan sequences have revealed that different amino acid substitutions have accumulated over years and have shown clustering with other Human Immunodeficiency Virus sequences. Single-nucleotide polymorphism (SNP) analysis has shown variations occurred in different regions at various frequencies, as per the need of the HIV genome for replication. The Human Immunodeficiency Virus (HIV) reads coverage map shows peak variation positions at various frequency levels of the Human Immunodeficiency Virus-1 (HIV-1) Sequence Read Archive (SRA) file. Its nucleotide range from 84000 to 98000 shows the highest frequency of SNPs. Human Immunodeficiency Virus (HIV-1) 454 (Roche) analysis has shown different expression patterns of different Human Immunodeficiency Virus (HIV) samples and Single-Nucleotide Polymorphism at different frequencies in the HIV population showed causing drug resistance abilities. The coverage curve map shows the two most coverage ranges of nucleotide sequences between ?80000-100000? and ?180000-200000? against the tag number of the same range between ?60-65? on the y-axis. The self-made program (SMP) taking Human Immunodeficiency Virus-1 (HIV-1) envelope protein sequence files from different countries conveyed information about their mutational changes, substitutions, transitions, trans-version, ratio of transition versus trans-version and silent mutation occurring at different sequences of nucleotide. The docking score between the protein 2NY1 and its inhibitor BMS-378806 revealed the strength of the binding ability between them.