HCDP: Hepatitis C Data Bank of Pakistan

  • Muhammad Shahzad Hazara University, Mansehra, Pakistan
  • Arif Iqbal Umar Hazara University, Mansehra, Pakistan
  • Syed Hamad Shirazi Hazara University, Mansehra, Pakistan
  • Muhammad Tariq Pervez Virtual University of Pakistan
  • Zakir Khan Hazara University, Mansehra, Pakistan
  • Waqas Yousaf Hazara University, Mansehra, Pakistan
Keywords: HCDP (Hepatitis C Data Bank of Pakistan),, PTM (Post Translational Modification), Genotype, Hepatitis C virus (HCV)

Abstract

Hepatitis C virus (HCV) is a blood born, positive, single stranded RNA strand and circular in shape. The hepatitis C virus is substantial threat to the public health and its frequency is increasing rapidly all over the world. Approximately 5 online databases are available related to Hepatitis C virus. All these databases mainly concerned their national level/specific demographic region strains for analysis. No HCV database available to find the HCV prevalence and distribution in Pakistan. We proposed a Hepatitis C virus database for Pakistani community, Hepatitis C Data Bank of Pakistan (HCDP). HCDP will be the first database that will holds HCV sequences obtained from Pakistani strains and HCV research publication by Pakistani researchers. We proposed a Hepatitis C Data Bank of Pakistan (HCDP) with an online interface. In addition to provision of annotated HCV sequences of Pakistani strains, HCDP allows the user to submit HCV sequences, find out N/O-linked glycosylation, Methylation, Ser/Tyr/Thr-phosphorylation, Methylation and ubiquitination sites in the protein sequences, motif/signature sub-sequences pattern, visual appearance of protein/nucleotide sequences for analysis of different sites, visual representation of multiple sequence alignments using colour code along with motif finding/conserved region in the sequence and analysing of graphical structure of phylogenetic tree. With the help of Format converter/Fasta generator tool user can convert sequence with formats of PhyLip, NEXUS, MSF, CLUSTAL and PIR into standard FASTA. It is also observed that genotype 3a (76%) is more prevalent followed by genotype 3 (13%). Geographic distribution reveals that rate of occurrence of HCV in Sindh and KPK is high with respect to other provinces. An annotated database of HCV genome sequences allows the researcher to investigate the structural and genetic variability of the sequences efficiently and effectively. HCDP is a specialized database that mainly focuses on the HCV strain from Pakistani community. It helps virologists in drug designing and vaccine development.

 

Author Biographies

Muhammad Shahzad, Hazara University, Mansehra, Pakistan

Department of Information Technology

Arif Iqbal Umar, Hazara University, Mansehra, Pakistan

Department of Information Technology

Syed Hamad Shirazi, Hazara University, Mansehra, Pakistan

Department of Information Technology

Muhammad Tariq Pervez, Virtual University of Pakistan

Department of Bioinformatics and Computational Biology

Zakir Khan, Hazara University, Mansehra, Pakistan

Department of Information Technology

Waqas Yousaf, Hazara University, Mansehra, Pakistan

Department of Information Technology

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Published
2019-12-31
How to Cite
Shahzad, M., Umar, A. I., Shirazi, S. H., Pervez, M. T., Khan, Z., & Yousaf, W. (2019, December 31). HCDP: Hepatitis C Data Bank of Pakistan. JOURNAL OF ENGINEERING AND APPLIED SCIENCES, 38(2). https://doi.org/https://doi.org/10.25211/jeas.v38i2.3142