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HCDP: HEPATITIS C DATA BANK OF PAKISTAN

 Muhammad Shahzad1, Arif Iqbal Umar1, Syed Hamad Shirazi1, Muhammad Tariq Pervez2*, Zakir Khan1, Waqas Yousaf1

 1 Department of Information Technology, Hazara University Mansehra, Pakistan,

2 Department of Bioinformatics and Computational Biology, Virtual University of Pakistan
*Corresponding author: m.tariq@vu.edu.pk

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.

 

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Journal of Engineering and Applied Sciences

June

Vol. 39, Iss. 1, pp. 01-126

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