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Protocol publication

[…] [The Current Study aimed to investigate the possible role of Heparanase protein (HPSE-1, [Entrez Pubmed ref|NP_001092010.1|, heparanase isoform 1 preproprotein [Homo sapiens]) in evolution by studying the phylogenetic relationship and divergence of HPSE-1 gene using computational methods. The Human HPSE protein sequences from various species were retrieved from GenBank database and were compared using sequence alignment. Multiple sequence alignment was done using Clustal-W with defaults and phylogenetic trees for the gene were built using neighbor-joining method as in BLAST 2.2.26+ version. A total of 112 BLAST hits were found for the heparanase query sequence and these hits showed putative conserved domain, Glyco_hydro_79n superfamily. We then narrowed down the search by manually deleting the proteins which were not HPSE-1. These sequences were then subjected to phylogenetic analyses using the PhyML and TreeDyn software. Our study indicated that HPSE-1 is a conserved protein in classes Mammalia, Aves, Amphibia, Actinopterygii and Insecta emphasizing its importance in the physiology of cell membranes. Occurrence of this gene in evolution with conserved sites strengthens the role of HPSE-1 gene and helps in better understanding the biochemical processes that may lead to cancer., Cancer remains an important cause of chronic illness. Better understanding of various genes and proteins and their implications at the cellular and molecular levels helps in identifying appropriate preventive/diagnostic measures. Studies in our lab on heparanase (HPSE-1 [Entrez Pubmed ref|NP_001092010.1|, heparanase i […]

Pipeline specifications

Software tools Clustal W, PhyML, TreeDyn
Organisms Homo sapiens
Diseases Neoplasms, Wiskott-Aldrich Syndrome