Comparative metagenomics analysis of palm oil mill effluent (POME) using three different bioinformatics pipelines

The substantial cost reduction and massive production of next-generation sequencing (NGS) data have contributed to the progress in the rapid growth of metagenomics. However, production of the massive amount of data by NGS has revealed the challenges in handling the existing bioinformatics tools rela...

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Main Authors:	Parman, Adibah, Mat Isa, Mohd Noor, Ben Belgacem, Farah Fadwa, Noorbatcha, Ibrahim Ali, Mohd. Salleh, Hamzah
Format:	Article
Language:	English English English
Published:	Faculty of Engineering, International Islamic University Malaysia 2019
Subjects:	TP Chemical technology TP248.13 Biotechnology
Online Access:	http://irep.iium.edu.my/72529/ http://irep.iium.edu.my/72529/ http://irep.iium.edu.my/72529/ http://irep.iium.edu.my/72529/1/72529_Comparative%20metagenomics%20analysis%20of%20palm%20oil.pdf http://irep.iium.edu.my/72529/7/72529_COMPARATIVE%20METAGENOMICS%20ANALYSIS%20OF%20PALM%20OIL%20MILL%20EFFLUENT%20%28POME%29%20USING%20THREE%20DIFFERENT%20BIOINFORMATICS%20PIPELINES_WOS.pdf http://irep.iium.edu.my/72529/8/72529_Comparative%20metagenomics%20analysis%20of%20palm%20oil_scopus.pdf

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recordtype	eprints
spelling	iium-725292019-11-24T10:58:16Z http://irep.iium.edu.my/72529/ Comparative metagenomics analysis of palm oil mill effluent (POME) using three different bioinformatics pipelines Parman, Adibah Mat Isa, Mohd Noor Ben Belgacem, Farah Fadwa Noorbatcha, Ibrahim Ali Mohd. Salleh, Hamzah TP Chemical technology TP248.13 Biotechnology The substantial cost reduction and massive production of next-generation sequencing (NGS) data have contributed to the progress in the rapid growth of metagenomics. However, production of the massive amount of data by NGS has revealed the challenges in handling the existing bioinformatics tools related to metagenomics. Therefore, in this research we have investigated an equal set of DNA metagenomics data from palm oil mill effluent (POME) sample using three different freeware bioinformatics pipelines’ websites of metagenomics RAST server (MG-RAST), Integrated Microbial Genomes with Microbiome Samples (IMG/M) and European Bioinformatics Institute (EBI) Metagenomics, in term of the taxonomic assignment and functional analysis. We found that MG-RAST is the quickest among these three pipelines. However, in term of analysis of results, IMG/M provides more variety of phylum with wider percent identities for taxonomical assignment and IMG/M provides the highest carbohydrates, amino acids, lipids, and coenzymes transport and metabolism functional annotation beside the highest in total number of glycoside hydrolase enzymes. Next, in identifying the conserved domain and family involved, EBI Metagenomics would be much more appropriate. All the three bioinformatics pipelines have their own specialties and can be used alternately or at the same time based on the user’s functional preference. Faculty of Engineering, International Islamic University Malaysia 2019-06-01 Article PeerReviewed application/pdf en http://irep.iium.edu.my/72529/1/72529_Comparative%20metagenomics%20analysis%20of%20palm%20oil.pdf application/pdf en http://irep.iium.edu.my/72529/7/72529_COMPARATIVE%20METAGENOMICS%20ANALYSIS%20OF%20PALM%20OIL%20MILL%20EFFLUENT%20%28POME%29%20USING%20THREE%20DIFFERENT%20BIOINFORMATICS%20PIPELINES_WOS.pdf application/pdf en http://irep.iium.edu.my/72529/8/72529_Comparative%20metagenomics%20analysis%20of%20palm%20oil_scopus.pdf Parman, Adibah and Mat Isa, Mohd Noor and Ben Belgacem, Farah Fadwa and Noorbatcha, Ibrahim Ali and Mohd. Salleh, Hamzah (2019) Comparative metagenomics analysis of palm oil mill effluent (POME) using three different bioinformatics pipelines. IIUM Engineering Journal, 20 (1). pp. 1-11. ISSN 1511-788X E-ISSN 2289-7860 https://journals.iium.edu.my/ejournal/index.php/iiumej/article/view/909/684 https://doi.org/10.31436/iiumej.v20i1.909
repository_type	Digital Repository
institution_category	Local University
institution	International Islamic University Malaysia
building	IIUM Repository
collection	Online Access
language	English English English
topic	TP Chemical technology TP248.13 Biotechnology
spellingShingle	TP Chemical technology TP248.13 Biotechnology Parman, Adibah Mat Isa, Mohd Noor Ben Belgacem, Farah Fadwa Noorbatcha, Ibrahim Ali Mohd. Salleh, Hamzah Comparative metagenomics analysis of palm oil mill effluent (POME) using three different bioinformatics pipelines
description	The substantial cost reduction and massive production of next-generation sequencing (NGS) data have contributed to the progress in the rapid growth of metagenomics. However, production of the massive amount of data by NGS has revealed the challenges in handling the existing bioinformatics tools related to metagenomics. Therefore, in this research we have investigated an equal set of DNA metagenomics data from palm oil mill effluent (POME) sample using three different freeware bioinformatics pipelines’ websites of metagenomics RAST server (MG-RAST), Integrated Microbial Genomes with Microbiome Samples (IMG/M) and European Bioinformatics Institute (EBI) Metagenomics, in term of the taxonomic assignment and functional analysis. We found that MG-RAST is the quickest among these three pipelines. However, in term of analysis of results, IMG/M provides more variety of phylum with wider percent identities for taxonomical assignment and IMG/M provides the highest carbohydrates, amino acids, lipids, and coenzymes transport and metabolism functional annotation beside the highest in total number of glycoside hydrolase enzymes. Next, in identifying the conserved domain and family involved, EBI Metagenomics would be much more appropriate. All the three bioinformatics pipelines have their own specialties and can be used alternately or at the same time based on the user’s functional preference.
format	Article
author	Parman, Adibah Mat Isa, Mohd Noor Ben Belgacem, Farah Fadwa Noorbatcha, Ibrahim Ali Mohd. Salleh, Hamzah
author_facet	Parman, Adibah Mat Isa, Mohd Noor Ben Belgacem, Farah Fadwa Noorbatcha, Ibrahim Ali Mohd. Salleh, Hamzah
author_sort	Parman, Adibah
title	Comparative metagenomics analysis of palm oil mill effluent (POME) using three different bioinformatics pipelines
title_short	Comparative metagenomics analysis of palm oil mill effluent (POME) using three different bioinformatics pipelines
title_full	Comparative metagenomics analysis of palm oil mill effluent (POME) using three different bioinformatics pipelines
title_fullStr	Comparative metagenomics analysis of palm oil mill effluent (POME) using three different bioinformatics pipelines
title_full_unstemmed	Comparative metagenomics analysis of palm oil mill effluent (POME) using three different bioinformatics pipelines
title_sort	comparative metagenomics analysis of palm oil mill effluent (pome) using three different bioinformatics pipelines
publisher	Faculty of Engineering, International Islamic University Malaysia
publishDate	2019
url	http://irep.iium.edu.my/72529/ http://irep.iium.edu.my/72529/ http://irep.iium.edu.my/72529/ http://irep.iium.edu.my/72529/1/72529_Comparative%20metagenomics%20analysis%20of%20palm%20oil.pdf http://irep.iium.edu.my/72529/7/72529_COMPARATIVE%20METAGENOMICS%20ANALYSIS%20OF%20PALM%20OIL%20MILL%20EFFLUENT%20%28POME%29%20USING%20THREE%20DIFFERENT%20BIOINFORMATICS%20PIPELINES_WOS.pdf http://irep.iium.edu.my/72529/8/72529_Comparative%20metagenomics%20analysis%20of%20palm%20oil_scopus.pdf
first_indexed	2023-09-18T21:42:45Z
last_indexed	2023-09-18T21:42:45Z
_version_	1777413249029898240

Comparative metagenomics analysis of palm oil mill effluent (POME) using three different bioinformatics pipelines

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