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      Bioinformatics Approaches for Human Gut Microbiome Research

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          Abstract

          The human gut microbiome has received great attention because many studies have revealed that it is associated with a variety of diseases. The extraordinary large datasets of microbiome studies indicate that bioinformatics approaches are crucial for their analyses. Here, we systematically reviewed bioinformatics tools that are commonly used in microbiome research, including a typical pipeline and software for sequence alignment, abundance profiling, enterotype determination, taxonomic diversity, identifying differentially abundant species/genes, gene cataloging, and functional analyses. We also reviewed the algorithms and methods used to define metagenomic species and co-abundance gene groups to expand our knowledge of unclassified and poorly understood gut microbes that are undocumented in the current genome databases. Additionally, we examined the methods used to identify metagenomic biomarkers based on the gut microbiome, which might help to expand the knowledge and approaches for disease detection and surveillance.

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          Most cited references41

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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              Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

              S Altschul (1997)
              The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
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                Author and article information

                Contributors
                Journal
                Infectious Diseases and Translational Medicine
                Infect. Dis. Transl. Med.
                Infect. Dis. Transl. Med.
                International Biological and Medical Journals Publishing House Co., Limited (Room E16, 3/f, Yongda Commercial Building, No.97, Bonham Stand (Sheung Wan), HongKong )
                2411-2917
                10 July 2016
                10 July 2016
                : 2
                : 2
                : 69-79
                Affiliations
                From RealBio Genomic Institute, Shanghai 200050, China
                From RealBio Genomic Institute, Shanghai 200050, China
                State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, Hangzhou 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
                From RealBio Genomic Institute, Shanghai 200050, China
                From RealBio Genomic Institute, Shanghai 200050, China
                From RealBio Genomic Institute, Shanghai 200050, China
                From RealBio Genomic Institute, Shanghai 200050, China
                From RealBio Genomic Institute, Shanghai 200050, China
                Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai District, Beijing 100071, China
                Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai District, Beijing 100071, China
                State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, Hangzhou 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
                Author notes
                Correspondence to: Nan Qin, Email: qinnan001@ 123456126.com ;
                Article
                10.11979/idtm.201602005
                900f9dff-f90d-4dce-bf33-f463145e166b

                This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                Page count
                Figures: 6, Tables: 3, References: 91, Pages: 11
                Product
                Categories
                Review

                Medicine,Infectious disease & Microbiology
                Bioinformatics approaches,Metagenomic biomarker,Human microbiome

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