English  |  正體中文  |  简体中文  |  Items with full text/Total items : 27320/39164
Visitors : 2474431      Online Users : 41
RC Version 4.0 © Powered By DSPACE, MIT. Enhanced by NTU Library IR team.
Scope Adv. Search
LoginUploadHelpAboutAdminister

Please use this identifier to cite or link to this item: http://ntour.ntou.edu.tw:8080/ir/handle/987654321/51198

Title: Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency
Authors: Weng FC
Su CH
Hsu MT
Wang TY
Tsai HK
Wang D
Contributors: 國立臺灣海洋大學:資訊工程學系
Keywords: Conserved sequence
Metagenome
Product binning
Metagenomics
BLAST Unassigned Dosage Form
DNA Barcoding, Taxonomic
Phylum (taxon)
Biopolymer Sequencing
PersonNameUse - assigned
Community
Herlitz Disease
Reading (activity)
Date: 2010-11
Issue Date: 2018-11-15T08:37:21Z
Publisher: BMC Bioinformatics
Abstract: Abstract:Background:
Investigation of metagenomes provides greater insight into uncultured microbial communities. The improvement in sequencing technology, which yields a large amount of sequence data, has led to major breakthroughs in the field. However, at present, taxonomic binning tools for metagenomes discard 30-40% of Sanger sequencing data due to the stringency of BLAST cut-offs. In an attempt to provide a comprehensive overview of metagenomic data, we re-analyzed the discarded metagenomes by using less stringent cut-offs. Additionally, we introduced a new criterion, namely, the evolutionary conservation of adjacency between neighboring genes. To evaluate the feasibility of our approach, we re-analyzed discarded contigs and singletons from several environments with different levels of complexity. We also compared the consistency between our taxonomic binning and those reported in the original studies.

RESULTS:
Among the discarded data, we found that 23.7 ± 3.9% of singletons and 14.1 ± 1.0% of contigs were assigned to taxa. The recovery rates for singletons were higher than those for contigs. The Pearson correlation coefficient revealed a high degree of similarity (0.94 ± 0.03 at the phylum rank and 0.80 ± 0.11 at the family rank) between the proposed taxonomic binning approach and those reported in original studies. In addition, an evaluation using simulated data demonstrated the reliability of the proposed approach.

CONCLUSIONS:
Our findings suggest that taking account of conserved neighboring gene adjacency improves taxonomic assignment when analyzing metagenomes using Sanger sequencing. In other words, utilizing the conserved gene order as a criterion will reduce the amount of data discarded when analyzing metagenomes.
Relation: 11 pp.565
URI: http://ntour.ntou.edu.tw:8080/ir/handle/987654321/51198
Appears in Collections:[資訊工程學系] 期刊論文

Files in This Item:

File Description SizeFormat
index.html0KbHTML7View/Open


All items in NTOUR are protected by copyright, with all rights reserved.

 


著作權政策宣告: 本網站之內容為國立臺灣海洋大學所收錄之機構典藏,無償提供學術研究與公眾教育等公益性使用,請合理使用本網站之內容,以尊重著作權人之權益。
網站維護: 海大圖資處 圖書系統組
DSpace Software Copyright © 2002-2004  MIT &  Hewlett-Packard  /   Enhanced by   NTU Library IR team Copyright ©   - Feedback