NGS-data analysis for netagenome cellulose- and Xylan- degrading enzymes finding

Abstract. For the aim of finding cellulose- and xylan-degrading enzymes needed in green industry to produce biofuel from plant biomass, a metagenomic DNA library from palm oil mill effluent (POME) was constructed and high-throughputly screened. The positive clones’ DNA were sequenced with next gener...

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Main Authors:	Ibrahim Ali, Noorbatcha, Hamzah, Mohd. Salleh
Format:	Conference or Workshop Item
Language:	English English English
Published:	2017
Subjects:	TP248.13 Biotechnology
Online Access:	http://irep.iium.edu.my/61696/ http://irep.iium.edu.my/61696/1/ARCSB2017%20presentation%20slides.pdf http://irep.iium.edu.my/61696/2/ARCSB2017%20-%20announcement.pdf http://irep.iium.edu.my/61696/3/arcsb_2017-programme.pdf

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recordtype	eprints
spelling	iium-616962018-02-03T08:50:58Z http://irep.iium.edu.my/61696/ NGS-data analysis for netagenome cellulose- and Xylan- degrading enzymes finding Ibrahim Ali, Noorbatcha Hamzah, Mohd. Salleh TP248.13 Biotechnology Abstract. For the aim of finding cellulose- and xylan-degrading enzymes needed in green industry to produce biofuel from plant biomass, a metagenomic DNA library from palm oil mill effluent (POME) was constructed and high-throughputly screened. The positive clones’ DNA were sequenced with next generation sequencing and raw data (short insert-paired) was analyzed with bioinformatic tools. First, the quality of 64.821.599 reverse and forward sequences of 101bp length raw data was identified using Fastqc. Then, raw data filtering was done by trimming low quality values and short reads and the vector sequences were removed and again the output was checked and the trimming was repeated until a high quality read sets was obtained. The second step was the de novo assembly of sequences to reconstruct 2900 contigs following de bruijn graph algorithm. Pre-assembled contigs were arranged in order, the distances between contigs were identified and oriented with SSPACE, where 2139 scaffolds have been reconstructed. 16386 genes have been identified after gene prediction using Prodigal and putative ID assignment with Blastp Vs NR protein. In these results, 17 cellulose-degrading enzymes and 2 xylan-degrading enzymes have been found. The genes encoding these enzymes will be recombinant to pBAD TOPO vector and cloned into TOP10 E. coli to express and characterize the enzymes for downstream processes. Key words: metagenomics, contig, scaffold, de novo assembly, de Bruijn, SSPACE, Prodigal, Blastp. 2017-11-22 Conference or Workshop Item PeerReviewed application/pdf en http://irep.iium.edu.my/61696/1/ARCSB2017%20presentation%20slides.pdf application/pdf en http://irep.iium.edu.my/61696/2/ARCSB2017%20-%20announcement.pdf application/pdf en http://irep.iium.edu.my/61696/3/arcsb_2017-programme.pdf Ibrahim Ali, Noorbatcha and Hamzah, Mohd. Salleh (2017) NGS-data analysis for netagenome cellulose- and Xylan- degrading enzymes finding. In: Asian Regional Conference on Systems Biology 2017 (ARCSB2017), Putrajaya Marriott Hotel, Malaysia. (Unpublished)
repository_type	Digital Repository
institution_category	Local University
institution	International Islamic University Malaysia
building	IIUM Repository
collection	Online Access
language	English English English
topic	TP248.13 Biotechnology
spellingShingle	TP248.13 Biotechnology Ibrahim Ali, Noorbatcha Hamzah, Mohd. Salleh NGS-data analysis for netagenome cellulose- and Xylan- degrading enzymes finding
description	Abstract. For the aim of finding cellulose- and xylan-degrading enzymes needed in green industry to produce biofuel from plant biomass, a metagenomic DNA library from palm oil mill effluent (POME) was constructed and high-throughputly screened. The positive clones’ DNA were sequenced with next generation sequencing and raw data (short insert-paired) was analyzed with bioinformatic tools. First, the quality of 64.821.599 reverse and forward sequences of 101bp length raw data was identified using Fastqc. Then, raw data filtering was done by trimming low quality values and short reads and the vector sequences were removed and again the output was checked and the trimming was repeated until a high quality read sets was obtained. The second step was the de novo assembly of sequences to reconstruct 2900 contigs following de bruijn graph algorithm. Pre-assembled contigs were arranged in order, the distances between contigs were identified and oriented with SSPACE, where 2139 scaffolds have been reconstructed. 16386 genes have been identified after gene prediction using Prodigal and putative ID assignment with Blastp Vs NR protein. In these results, 17 cellulose-degrading enzymes and 2 xylan-degrading enzymes have been found. The genes encoding these enzymes will be recombinant to pBAD TOPO vector and cloned into TOP10 E. coli to express and characterize the enzymes for downstream processes. Key words: metagenomics, contig, scaffold, de novo assembly, de Bruijn, SSPACE, Prodigal, Blastp.
format	Conference or Workshop Item
author	Ibrahim Ali, Noorbatcha Hamzah, Mohd. Salleh
author_facet	Ibrahim Ali, Noorbatcha Hamzah, Mohd. Salleh
author_sort	Ibrahim Ali, Noorbatcha
title	NGS-data analysis for netagenome cellulose- and Xylan- degrading enzymes finding
title_short	NGS-data analysis for netagenome cellulose- and Xylan- degrading enzymes finding
title_full	NGS-data analysis for netagenome cellulose- and Xylan- degrading enzymes finding
title_fullStr	NGS-data analysis for netagenome cellulose- and Xylan- degrading enzymes finding
title_full_unstemmed	NGS-data analysis for netagenome cellulose- and Xylan- degrading enzymes finding
title_sort	ngs-data analysis for netagenome cellulose- and xylan- degrading enzymes finding
publishDate	2017
url	http://irep.iium.edu.my/61696/ http://irep.iium.edu.my/61696/1/ARCSB2017%20presentation%20slides.pdf http://irep.iium.edu.my/61696/2/ARCSB2017%20-%20announcement.pdf http://irep.iium.edu.my/61696/3/arcsb_2017-programme.pdf
first_indexed	2023-09-18T21:27:29Z
last_indexed	2023-09-18T21:27:29Z
_version_	1777412288446201856

NGS-data analysis for netagenome cellulose- and Xylan- degrading enzymes finding

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