HRE Finder: A Tool for Quarrying Hypoxia-Response Element in Genomic Sequences

Iliyas Rashid; Naresh Sahebrao Nagpure; Prachi Srivastava; Ajey Kumar Pathak; Ravindra Kumar; Vishwamitra Singh Baisvar; Mahender Singh; Basdeo Kushwaha

doi:https://doi.org/10.20546/ijcmas.2017.607.190

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Original Research Articles Volume : 6, Issue:7, July, 2017

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Int.J.Curr.Microbiol.App.Sci.2017.6(7): 1580-1586

DOI: https://doi.org/10.20546/ijcmas.2017.607.190

HRE Finder: A Tool for Quarrying Hypoxia-Response Element in Genomic Sequences

Iliyas Rashid^1,2, Naresh Sahebrao Nagpure³, Prachi Srivastava², Ajey Kumar Pathak¹*, Ravindra Kumar¹, Vishwamitra Singh Baisvar¹, Mahender Singh¹ and Basdeo Kushwaha¹

¹Molecular Biology and Biotechnology Division, ICAR- National Bureau of Fish Genetic Resources, Lucknow- 226 002, Uttar Pradesh, India
²AMITY Institute of Biotechnology, AMITY University Uttar Pradesh, Lucknow-226 028,Uttar Pradesh, India
³Fish Genetics and Biotechnology Division, ICAR- Central Institute of Fisheries Education, Mumbai-400 061, Maharashtra, India

^*Corresponding author

Abstract:

During hypoxia, the hypoxia inducible factor (HIF) binds to hypoxia-response elements (HRE) and induces the expression of hypoxia-inducible genes (HIG). A functionally active HRE typically contains an adjacent hypoxia ancillary sequence (HAS) in its downstream within the space of 7-15 nt. Here, a computational tool 'HRE Finder' is discussed using an example data set. The tool provides the ability for mining canonical HREs and predicting functional HREs in the upstream region of genes, which can be an indispensable tool for genome-wide analysis and identification of hypoxia inducible genes in vertebrates.

Keywords: Database, Hypoxia inducible factor, Hypoxia response element, Hypoxia, Transcription, Gene, Enhancer, Search algorithm.

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Iliyas Rashid, Naresh Sahebrao Nagpure, Prachi Srivastava, Ajey Kumar Pathak, Ravindra Kumar, Vishwamitra Singh Baisvar, Mahender Singh and Basdeo Kushwaha. 2017. HRE Finder: A Tool for Quarrying Hypoxia-Response Element in Genomic Sequences.Int.J.Curr.Microbiol.App.Sci. 6(7): 1580-1586. doi: https://doi.org/10.20546/ijcmas.2017.607.190

Copyright: This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike license.

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Original Research Articles Volume : 6, Issue:7, July, 2017

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