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A Phylogenetic analysis of Heparanase (HPSE) gene
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 H...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Biomedical Informatics
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3374371/ https://www.ncbi.nlm.nih.gov/pubmed/22715311 http://dx.doi.org/10.6026/97320630008415 |
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author | Shaik, Abjal Pasha Alsaeed, Abbas H Sultana, Asma |
author_facet | Shaik, Abjal Pasha Alsaeed, Abbas H Sultana, Asma |
author_sort | Shaik, Abjal Pasha |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3374371 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Biomedical Informatics |
record_format | MEDLINE/PubMed |
spelling | pubmed-33743712012-06-19 A Phylogenetic analysis of Heparanase (HPSE) gene Shaik, Abjal Pasha Alsaeed, Abbas H Sultana, Asma Bioinformation Hypothesis 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. Biomedical Informatics 2012-05-15 /pmc/articles/PMC3374371/ /pubmed/22715311 http://dx.doi.org/10.6026/97320630008415 Text en © 2012 Biomedical Informatics This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited. |
spellingShingle | Hypothesis Shaik, Abjal Pasha Alsaeed, Abbas H Sultana, Asma A Phylogenetic analysis of Heparanase (HPSE) gene |
title | A Phylogenetic analysis of Heparanase (HPSE) gene |
title_full | A Phylogenetic analysis of Heparanase (HPSE) gene |
title_fullStr | A Phylogenetic analysis of Heparanase (HPSE) gene |
title_full_unstemmed | A Phylogenetic analysis of Heparanase (HPSE) gene |
title_short | A Phylogenetic analysis of Heparanase (HPSE) gene |
title_sort | phylogenetic analysis of heparanase (hpse) gene |
topic | Hypothesis |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3374371/ https://www.ncbi.nlm.nih.gov/pubmed/22715311 http://dx.doi.org/10.6026/97320630008415 |
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